diff --git a/muted-tests.yml b/muted-tests.yml
index ec7bb6ab41885..17a7b26d1c091 100644
--- a/muted-tests.yml
+++ b/muted-tests.yml
@@ -1,77 +1,18 @@
 tests:
-- class: org.elasticsearch.smoketest.DocsClientYamlTestSuiteIT
-  method: test {yaml=reference/esql/esql-async-query-api/line_17}
-  issue: https://github.com/elastic/elasticsearch/issues/109260
 - class: "org.elasticsearch.client.RestClientSingleHostIntegTests"
   issue: "https://github.com/elastic/elasticsearch/issues/102717"
   method: "testRequestResetAndAbort"
-- class: org.elasticsearch.index.store.FsDirectoryFactoryTests
-  method: testStoreDirectory
-  issue: https://github.com/elastic/elasticsearch/issues/110210
-- class: org.elasticsearch.index.store.FsDirectoryFactoryTests
-  method: testPreload
-  issue: https://github.com/elastic/elasticsearch/issues/110211
-- class: org.elasticsearch.upgrades.SecurityIndexRolesMetadataMigrationIT
-  method: testMetadataMigratedAfterUpgrade
-  issue: https://github.com/elastic/elasticsearch/issues/110232
-- class: org.elasticsearch.xpack.security.authz.store.NativePrivilegeStoreCacheTests
-  method: testPopulationOfCacheWhenLoadingPrivilegesForAllApplications
-  issue: https://github.com/elastic/elasticsearch/issues/110789
-- class: org.elasticsearch.xpack.searchablesnapshots.cache.common.CacheFileTests
-  method: testCacheFileCreatedAsSparseFile
-  issue: https://github.com/elastic/elasticsearch/issues/110801
-- class: org.elasticsearch.nativeaccess.VectorSystemPropertyTests
-  method: testSystemPropertyDisabled
-  issue: https://github.com/elastic/elasticsearch/issues/110949
-- class: org.elasticsearch.xpack.security.authc.oidc.OpenIdConnectAuthIT
-  method: testAuthenticateWithImplicitFlow
-  issue: https://github.com/elastic/elasticsearch/issues/111191
-- class: org.elasticsearch.xpack.security.authc.oidc.OpenIdConnectAuthIT
-  method: testAuthenticateWithCodeFlowAndClientPost
-  issue: https://github.com/elastic/elasticsearch/issues/111396
 - class: org.elasticsearch.xpack.restart.FullClusterRestartIT
   method: testSingleDoc {cluster=UPGRADED}
   issue: https://github.com/elastic/elasticsearch/issues/111434
 - class: org.elasticsearch.xpack.restart.FullClusterRestartIT
   method: testDataStreams {cluster=UPGRADED}
   issue: https://github.com/elastic/elasticsearch/issues/111448
-- class: org.elasticsearch.search.SearchServiceTests
-  issue: https://github.com/elastic/elasticsearch/issues/111529
-- class: org.elasticsearch.upgrades.FullClusterRestartIT
-  method: testSnapshotRestore {cluster=UPGRADED}
-  issue: https://github.com/elastic/elasticsearch/issues/111798
-- class: org.elasticsearch.xpack.inference.InferenceRestIT
-  method: test {p0=inference/80_random_rerank_retriever/Random rerank retriever predictably shuffles results}
-  issue: https://github.com/elastic/elasticsearch/issues/111999
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testDeleteJobAfterMissingIndex
-  issue: https://github.com/elastic/elasticsearch/issues/112088
 - class: org.elasticsearch.smoketest.WatcherYamlRestIT
   method: test {p0=watcher/usage/10_basic/Test watcher usage stats output}
   issue: https://github.com/elastic/elasticsearch/issues/112189
-- class: org.elasticsearch.xpack.test.rest.XPackRestIT
-  method: test {p0=ml/inference_processor/Test create processor with missing mandatory fields}
-  issue: https://github.com/elastic/elasticsearch/issues/112191
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testDeleteJobAsync
-  issue: https://github.com/elastic/elasticsearch/issues/112212
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testMultiIndexDelete
-  issue: https://github.com/elastic/elasticsearch/issues/112381
-- class: org.elasticsearch.xpack.esql.expression.function.aggregate.SpatialCentroidTests
-  method: "testAggregateIntermediate {TestCase=<geo_point> #2}"
-  issue: https://github.com/elastic/elasticsearch/issues/112461
-- class: org.elasticsearch.xpack.esql.expression.function.aggregate.SpatialCentroidTests
-  method: testAggregateIntermediate {TestCase=<geo_point>}
-  issue: https://github.com/elastic/elasticsearch/issues/112463
-- class: org.elasticsearch.xpack.inference.external.http.RequestBasedTaskRunnerTests
-  method: testLoopOneAtATime
-  issue: https://github.com/elastic/elasticsearch/issues/112471
 - class: org.elasticsearch.ingest.geoip.IngestGeoIpClientYamlTestSuiteIT
   issue: https://github.com/elastic/elasticsearch/issues/111497
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testPutJob_GivenFarequoteConfig
-  issue: https://github.com/elastic/elasticsearch/issues/112382
 - class: org.elasticsearch.packaging.test.PackagesSecurityAutoConfigurationTests
   method: test20SecurityNotAutoConfiguredOnReInstallation
   issue: https://github.com/elastic/elasticsearch/issues/112635
@@ -87,21 +28,6 @@ tests:
 - class: org.elasticsearch.xpack.sql.qa.single_node.JdbcSqlSpecIT
   method: test {case-functions.testUcaseInline3}
   issue: https://github.com/elastic/elasticsearch/issues/112643
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testDelete_multipleRequest
-  issue: https://github.com/elastic/elasticsearch/issues/112701
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testCreateJobInSharedIndexUpdatesMapping
-  issue: https://github.com/elastic/elasticsearch/issues/112729
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testGetJob_GivenNoSuchJob
-  issue: https://github.com/elastic/elasticsearch/issues/112730
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testDeleteJobAfterMissingAliases
-  issue: https://github.com/elastic/elasticsearch/issues/112823
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testCreateJob_WithClashingFieldMappingsFails
-  issue: https://github.com/elastic/elasticsearch/issues/113046
 - class: org.elasticsearch.xpack.sql.qa.security.JdbcSqlSpecIT
   method: test {case-functions.testUcaseInline1}
   issue: https://github.com/elastic/elasticsearch/issues/112641
@@ -114,18 +40,12 @@ tests:
 - class: org.elasticsearch.xpack.sql.qa.security.JdbcSqlSpecIT
   method: test {case-functions.testSelectInsertWithLcaseAndLengthWithOrderBy}
   issue: https://github.com/elastic/elasticsearch/issues/112642
-- class: org.elasticsearch.xpack.inference.rest.ServerSentEventsRestActionListenerTests
-  method: testResponse
-  issue: https://github.com/elastic/elasticsearch/issues/113148
 - class: org.elasticsearch.packaging.test.WindowsServiceTests
   method: test30StartStop
   issue: https://github.com/elastic/elasticsearch/issues/113160
 - class: org.elasticsearch.packaging.test.WindowsServiceTests
   method: test33JavaChanged
   issue: https://github.com/elastic/elasticsearch/issues/113177
-- class: org.elasticsearch.xpack.inference.rest.ServerSentEventsRestActionListenerTests
-  method: testErrorMidStream
-  issue: https://github.com/elastic/elasticsearch/issues/113179
 - class: org.elasticsearch.smoketest.MlWithSecurityIT
   method: test {yaml=ml/sparse_vector_search/Test sparse_vector search with query vector and pruning config}
   issue: https://github.com/elastic/elasticsearch/issues/108997
@@ -138,27 +58,6 @@ tests:
 - class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
   method: test {p0=mtermvectors/10_basic/Tests catching other exceptions per item}
   issue: https://github.com/elastic/elasticsearch/issues/113325
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testDeleteJob_TimingStatsDocumentIsDeleted
-  issue: https://github.com/elastic/elasticsearch/issues/113370
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=search/500_date_range/from, to, include_lower, include_upper deprecated}
-  issue: https://github.com/elastic/elasticsearch/pull/113286
-- class: org.elasticsearch.index.mapper.extras.TokenCountFieldMapperTests
-  method: testBlockLoaderFromRowStrideReaderWithSyntheticSource
-  issue: https://github.com/elastic/elasticsearch/issues/113427
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testOutOfOrderData
-  issue: https://github.com/elastic/elasticsearch/issues/113477
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testCreateJobsWithIndexNameOption
-  issue: https://github.com/elastic/elasticsearch/issues/113528
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=search/180_locale_dependent_mapping/Test Index and Search locale dependent mappings / dates}
-  issue: https://github.com/elastic/elasticsearch/issues/113537
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testCantCreateJobWithSameID
-  issue: https://github.com/elastic/elasticsearch/issues/113581
 - class: org.elasticsearch.integration.KibanaUserRoleIntegTests
   method: testFieldMappings
   issue: https://github.com/elastic/elasticsearch/issues/113592
@@ -168,185 +67,183 @@ tests:
 - class: org.elasticsearch.xpack.transform.integration.TransformIT
   method: testStopWaitForCheckpoint
   issue: https://github.com/elastic/elasticsearch/issues/106113
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=search/540_ignore_above_synthetic_source/ignore_above mapping level setting on arrays}
-  issue: https://github.com/elastic/elasticsearch/issues/113648
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testGetJobs_GivenMultipleJobs
-  issue: https://github.com/elastic/elasticsearch/issues/113654
-- class: org.elasticsearch.xpack.ml.integration.MlJobIT
-  method: testGetJobs_GivenSingleJob
-  issue: https://github.com/elastic/elasticsearch/issues/113655
-- class: org.elasticsearch.xpack.esql.expression.function.scalar.convert.ToDateNanosTests
-  issue: https://github.com/elastic/elasticsearch/issues/113661
-- class: org.elasticsearch.search.retriever.RankDocsRetrieverBuilderTests
-  method: testRewrite
-  issue: https://github.com/elastic/elasticsearch/issues/114467
-- class: org.elasticsearch.gradle.internal.PublishPluginFuncTest
-  issue: https://github.com/elastic/elasticsearch/issues/114492
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=indices.split/40_routing_partition_size/nested}
-  issue: https://github.com/elastic/elasticsearch/issues/113842
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=indices.split/40_routing_partition_size/more than 1}
-  issue: https://github.com/elastic/elasticsearch/issues/113841
 - class: org.elasticsearch.kibana.KibanaThreadPoolIT
   method: testBlockedThreadPoolsRejectUserRequests
   issue: https://github.com/elastic/elasticsearch/issues/113939
-- class: org.elasticsearch.xpack.inference.TextEmbeddingCrudIT
-  method: testPutE5WithTrainedModelAndInference
-  issue: https://github.com/elastic/elasticsearch/issues/114023
 - class: org.elasticsearch.xpack.inference.TextEmbeddingCrudIT
   method: testPutE5Small_withPlatformAgnosticVariant
   issue: https://github.com/elastic/elasticsearch/issues/113983
-- class: org.elasticsearch.datastreams.LazyRolloverDuringDisruptionIT
-  method: testRolloverIsExecutedOnce
-  issue: https://github.com/elastic/elasticsearch/issues/112634
-- class: org.elasticsearch.xpack.rank.rrf.RRFRankClientYamlTestSuiteIT
-  method: test {yaml=rrf/800_rrf_with_text_similarity_reranker_retriever/explain using rrf retriever and text-similarity}
-  issue: https://github.com/elastic/elasticsearch/issues/114757
-- class: org.elasticsearch.xpack.remotecluster.RemoteClusterSecurityWithApmTracingRestIT
-  method: testTracingCrossCluster
-  issue: https://github.com/elastic/elasticsearch/issues/112731
+- class: org.elasticsearch.xpack.inference.TextEmbeddingCrudIT
+  method: testPutE5WithTrainedModelAndInference
+  issue: https://github.com/elastic/elasticsearch/issues/114023
 - class: org.elasticsearch.xpack.inference.TextEmbeddingCrudIT
   method: testPutE5Small_withPlatformSpecificVariant
   issue: https://github.com/elastic/elasticsearch/issues/113950
 - class: org.elasticsearch.smoketest.DocsClientYamlTestSuiteIT
   method: test {yaml=reference/rest-api/usage/line_38}
   issue: https://github.com/elastic/elasticsearch/issues/113694
-- class: org.elasticsearch.test.rest.yaml.RcsCcsCommonYamlTestSuiteIT
-  method: test {p0=search.vectors/42_knn_search_int4_flat/Vector similarity with filter only}
-  issue: https://github.com/elastic/elasticsearch/issues/115475
-- class: org.elasticsearch.reservedstate.service.FileSettingsServiceTests
-  method: testProcessFileChanges
-  issue: https://github.com/elastic/elasticsearch/issues/115280
+- class: org.elasticsearch.xpack.remotecluster.RemoteClusterSecurityWithApmTracingRestIT
+  method: testTracingCrossCluster
+  issue: https://github.com/elastic/elasticsearch/issues/112731
 - class: org.elasticsearch.xpack.inference.DefaultEndPointsIT
   method: testInferDeploysDefaultE5
   issue: https://github.com/elastic/elasticsearch/issues/115361
-- class: org.elasticsearch.xpack.inference.InferenceCrudIT
-  method: testSupportedStream
-  issue: https://github.com/elastic/elasticsearch/issues/113430
-- class: org.elasticsearch.xpack.spatial.search.GeoGridAggAndQueryConsistencyIT
-  method: testGeoShapeGeoHash
-  issue: https://github.com/elastic/elasticsearch/issues/115664
-- class: org.elasticsearch.indices.mapping.UpdateMappingIntegrationIT
-  issue: https://github.com/elastic/elasticsearch/issues/116126
-- class: org.elasticsearch.xpack.ml.integration.DatafeedJobsRestIT
-  issue: https://github.com/elastic/elasticsearch/issues/111319
-- class: org.elasticsearch.upgrades.FullClusterRestartIT
-  method: testSnapshotRestore {cluster=OLD}
-  issue: https://github.com/elastic/elasticsearch/issues/111777
+- class: org.elasticsearch.xpack.restart.MLModelDeploymentFullClusterRestartIT
+  method: testDeploymentSurvivesRestart {cluster=UPGRADED}
+  issue: https://github.com/elastic/elasticsearch/issues/115528
+- class: org.elasticsearch.action.update.UpdateResponseTests
+  method: testToAndFromXContent
+  issue: https://github.com/elastic/elasticsearch/issues/115689
+- class: org.elasticsearch.xpack.shutdown.NodeShutdownIT
+  method: testStalledShardMigrationProperlyDetected
+  issue: https://github.com/elastic/elasticsearch/issues/115697
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=transform/transforms_start_stop/Verify start transform reuses destination index}
+  issue: https://github.com/elastic/elasticsearch/issues/115808
+- class: org.elasticsearch.search.StressSearchServiceReaperIT
+  method: testStressReaper
+  issue: https://github.com/elastic/elasticsearch/issues/115816
+- class: org.elasticsearch.search.SearchServiceTests
+  method: testParseSourceValidation
+  issue: https://github.com/elastic/elasticsearch/issues/115936
+- class: org.elasticsearch.xpack.application.connector.ConnectorIndexServiceTests
+  issue: https://github.com/elastic/elasticsearch/issues/116087
+- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
+  method: test {p0=cat.shards/10_basic/Help}
+  issue: https://github.com/elastic/elasticsearch/issues/116110
 - class: org.elasticsearch.xpack.ml.integration.DatafeedJobsRestIT
   method: testLookbackWithIndicesOptions
   issue: https://github.com/elastic/elasticsearch/issues/116127
-- class: org.elasticsearch.xpack.restart.CoreFullClusterRestartIT
-  method: testSnapshotRestore {cluster=UPGRADED}
-  issue: https://github.com/elastic/elasticsearch/issues/111799
-- class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
-  method: test {p0=search/380_sort_segments_on_timestamp/Test that index segments are NOT sorted on timestamp field when @timestamp field is dynamically added}
-  issue: https://github.com/elastic/elasticsearch/issues/116221
-- class: org.elasticsearch.ingest.common.IngestCommonClientYamlTestSuiteIT
-  method: test {yaml=ingest/310_reroute_processor/Test remove then add reroute processor with and without lazy rollover}
-  issue: https://github.com/elastic/elasticsearch/issues/116158
-- class: org.elasticsearch.ingest.common.IngestCommonClientYamlTestSuiteIT
-  method: test {yaml=ingest/310_reroute_processor/Test data stream with lazy rollover obtains pipeline from template}
-  issue: https://github.com/elastic/elasticsearch/issues/116157
-- class: org.elasticsearch.ingest.geoip.EnterpriseGeoIpDownloaderIT
-  method: testEnterpriseDownloaderTask
-  issue: https://github.com/elastic/elasticsearch/issues/115163
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=transform/transforms_start_stop/Test start already started transform}
+  issue: https://github.com/elastic/elasticsearch/issues/98802
+- class: org.elasticsearch.action.search.SearchPhaseControllerTests
+  method: testProgressListener
+  issue: https://github.com/elastic/elasticsearch/issues/116149
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=terms_enum/10_basic/Test security}
+  issue: https://github.com/elastic/elasticsearch/issues/116178
+- class: org.elasticsearch.search.basic.SearchWithRandomDisconnectsIT
+  method: testSearchWithRandomDisconnects
+  issue: https://github.com/elastic/elasticsearch/issues/116175
 - class: org.elasticsearch.xpack.deprecation.DeprecationHttpIT
   method: testDeprecatedSettingsReturnWarnings
   issue: https://github.com/elastic/elasticsearch/issues/108628
-- class: org.elasticsearch.xpack.apmdata.APMYamlTestSuiteIT
-  method: test {yaml=/10_apm/Test template reinstallation}
-  issue: https://github.com/elastic/elasticsearch/issues/116445
-- class: org.elasticsearch.action.admin.HotThreadsIT
-  method: testHotThreadsDontFail
-  issue: https://github.com/elastic/elasticsearch/issues/115754
-- class: org.elasticsearch.action.search.PointInTimeIT
-  method: testPITTiebreak
-  issue: https://github.com/elastic/elasticsearch/issues/115810
-- class: org.elasticsearch.xpack.esql.qa.mixed.EsqlClientYamlIT
-  method: test {p0=esql/61_enrich_ip/IP strings}
-  issue: https://github.com/elastic/elasticsearch/issues/116529
+- class: org.elasticsearch.action.search.SearchQueryThenFetchAsyncActionTests
+  method: testBottomFieldSort
+  issue: https://github.com/elastic/elasticsearch/issues/116249
+- class: org.elasticsearch.xpack.shutdown.NodeShutdownIT
+  method: testAllocationPreventedForRemoval
+  issue: https://github.com/elastic/elasticsearch/issues/116363
+- class: org.elasticsearch.xpack.downsample.ILMDownsampleDisruptionIT
+  method: testILMDownsampleRollingRestart
+  issue: https://github.com/elastic/elasticsearch/issues/114233
+- class: org.elasticsearch.reservedstate.service.FileSettingsServiceTests
+  method: testInvalidJSON
+  issue: https://github.com/elastic/elasticsearch/issues/116521
 - class: org.elasticsearch.xpack.searchablesnapshots.SearchableSnapshotsCanMatchOnCoordinatorIntegTests
   method: testSearchableSnapshotShardsAreSkippedBySearchRequestWithoutQueryingAnyNodeWhenTheyAreOutsideOfTheQueryRange
   issue: https://github.com/elastic/elasticsearch/issues/116523
-- class: org.elasticsearch.xpack.inference.DefaultEndPointsIT
-  method: testInferDeploysDefaultElser
-  issue: https://github.com/elastic/elasticsearch/issues/114913
-- class: org.elasticsearch.threadpool.SimpleThreadPoolIT
-  method: testThreadPoolMetrics
-  issue: https://github.com/elastic/elasticsearch/issues/108320
-- class: org.elasticsearch.xpack.esql.qa.mixed.EsqlClientYamlIT
-  method: test {p0=esql/60_enrich/Enrich on keyword with fields alias}
-  issue: https://github.com/elastic/elasticsearch/issues/116592
-- class: org.elasticsearch.xpack.esql.qa.mixed.EsqlClientYamlIT
-  method: test {p0=esql/60_enrich/Enrich on keyword with fields}
-  issue: https://github.com/elastic/elasticsearch/issues/116593
-- class: org.elasticsearch.xpack.spatial.search.GeoGridAggAndQueryConsistencyIT
-  method: testGeoShapeGeoTile
-  issue: https://github.com/elastic/elasticsearch/issues/115717
-- class: org.elasticsearch.search.StressSearchServiceReaperIT
-  method: testStressReaper
-  issue: https://github.com/elastic/elasticsearch/issues/115816
-- class: org.elasticsearch.xpack.spatial.search.GeoGridAggAndQueryConsistencyIT
-  method: testGeoShapeGeoHex
-  issue: https://github.com/elastic/elasticsearch/issues/115705
-- class: org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNoDocValues SYNC}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
-- class: org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNoDocValues ASYNC}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
-- class: org.elasticsearch.xpack.esql.ccq.MultiClusterSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNoDocValues}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
-- class: org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNotIndexedNorDocValues SYNC}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
-- class: org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNotIndexedNorDocValues ASYNC}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
-- class: org.elasticsearch.xpack.esql.ccq.MultiClusterSpecIT
-  method: test {spatial.CentroidFromAirportsAfterIntersectsCompoundPredicateNotIndexedNorDocValues}
-  issue: https://github.com/elastic/elasticsearch/issues/116945
+- class: org.elasticsearch.reservedstate.service.RepositoriesFileSettingsIT
+  method: testSettingsApplied
+  issue: https://github.com/elastic/elasticsearch/issues/116694
+- class: org.elasticsearch.xpack.security.authc.ldap.ActiveDirectoryGroupsResolverTests
+  issue: https://github.com/elastic/elasticsearch/issues/116182
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=snapshot/20_operator_privileges_disabled/Operator only settings can be set and restored by non-operator user when operator privileges is disabled}
+  issue: https://github.com/elastic/elasticsearch/issues/116775
+- class: org.elasticsearch.xpack.searchablesnapshots.hdfs.SecureHdfsSearchableSnapshotsIT
+  issue: https://github.com/elastic/elasticsearch/issues/116851
 - class: org.elasticsearch.search.basic.SearchWithRandomIOExceptionsIT
   method: testRandomDirectoryIOExceptions
   issue: https://github.com/elastic/elasticsearch/issues/114824
-- class: org.elasticsearch.xpack.application.CohereServiceUpgradeIT
-  method: testRerank {upgradedNodes=1}
-  issue: https://github.com/elastic/elasticsearch/issues/116973
-- class: org.elasticsearch.xpack.application.CohereServiceUpgradeIT
-  method: testCohereEmbeddings {upgradedNodes=1}
-  issue: https://github.com/elastic/elasticsearch/issues/116974
-- class: org.elasticsearch.xpack.application.CohereServiceUpgradeIT
-  method: testCohereEmbeddings {upgradedNodes=2}
-  issue: https://github.com/elastic/elasticsearch/issues/116975
+- class: org.elasticsearch.xpack.apmdata.APMYamlTestSuiteIT
+  method: test {yaml=/10_apm/Test template reinstallation}
+  issue: https://github.com/elastic/elasticsearch/issues/116445
+- class: org.elasticsearch.xpack.inference.DefaultEndPointsIT
+  method: testMultipleInferencesTriggeringDownloadAndDeploy
+  issue: https://github.com/elastic/elasticsearch/issues/117208
+- class: org.elasticsearch.ingest.geoip.EnterpriseGeoIpDownloaderIT
+  method: testEnterpriseDownloaderTask
+  issue: https://github.com/elastic/elasticsearch/issues/115163
+- class: org.elasticsearch.versioning.ConcurrentSeqNoVersioningIT
+  method: testSeqNoCASLinearizability
+  issue: https://github.com/elastic/elasticsearch/issues/117249
+- class: org.elasticsearch.discovery.ClusterDisruptionIT
+  method: testAckedIndexing
+  issue: https://github.com/elastic/elasticsearch/issues/117024
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=snapshot/10_basic/Create a source only snapshot and then restore it}
+  issue: https://github.com/elastic/elasticsearch/issues/117295
 - class: org.elasticsearch.xpack.searchablesnapshots.RetrySearchIntegTests
   method: testRetryPointInTime
   issue: https://github.com/elastic/elasticsearch/issues/117116
+- class: org.elasticsearch.xpack.inference.DefaultEndPointsIT
+  method: testInferDeploysDefaultElser
+  issue: https://github.com/elastic/elasticsearch/issues/114913
 - class: org.elasticsearch.xpack.inference.InferenceRestIT
   method: test {p0=inference/40_semantic_text_query/Query a field that uses the default ELSER 2 endpoint}
   issue: https://github.com/elastic/elasticsearch/issues/117027
 - class: org.elasticsearch.xpack.inference.InferenceRestIT
   method: test {p0=inference/30_semantic_text_inference/Calculates embeddings using the default ELSER 2 endpoint}
   issue: https://github.com/elastic/elasticsearch/issues/117349
-- class: org.elasticsearch.search.basic.SearchWithRandomDisconnectsIT
-  method: testSearchWithRandomDisconnects
-  issue: https://github.com/elastic/elasticsearch/issues/116175
-- class: org.elasticsearch.action.search.SearchQueryThenFetchAsyncActionTests
-  method: testMinimumVersionBetweenNewAndOldVersion
-  issue: https://github.com/elastic/elasticsearch/issues/117485
-- class: org.elasticsearch.discovery.ClusterDisruptionIT
-  method: testAckedIndexing
-  issue: https://github.com/elastic/elasticsearch/issues/117024
-- class: org.elasticsearch.xpack.inference.DefaultEndPointsIT
-  method: testMultipleInferencesTriggeringDownloadAndDeploy
-  issue: https://github.com/elastic/elasticsearch/issues/117208
+- class: org.elasticsearch.xpack.test.rest.XPackRestIT
+  method: test {p0=transform/transforms_reset/Test reset running transform}
+  issue: https://github.com/elastic/elasticsearch/issues/117473
+- class: org.elasticsearch.repositories.s3.RepositoryS3EcsClientYamlTestSuiteIT
+  issue: https://github.com/elastic/elasticsearch/issues/117525
 - class: org.elasticsearch.backwards.MixedClusterClientYamlTestSuiteIT
   method: test {p0=synonyms/90_synonyms_reloading_for_synset/Reload analyzers for specific synonym set}
   issue: https://github.com/elastic/elasticsearch/issues/116777
+- class: org.elasticsearch.reservedstate.service.FileSettingsServiceTests
+  method: testStopWorksInMiddleOfProcessing
+  issue: https://github.com/elastic/elasticsearch/issues/117591
+- class: "org.elasticsearch.xpack.esql.qa.multi_node.EsqlSpecIT"
+  method: "test {scoring.*}"
+  issue: https://github.com/elastic/elasticsearch/issues/117641
+- class: "org.elasticsearch.xpack.esql.qa.single_node.EsqlSpecIT"
+  method: "test {scoring.*}"
+  issue: https://github.com/elastic/elasticsearch/issues/117641
+- class: "org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT"
+  method: "test {scoring.*}"
+  issue: https://github.com/elastic/elasticsearch/issues/117641
+- class: org.elasticsearch.xpack.inference.InferenceCrudIT
+  method: testSupportedStream
+  issue: https://github.com/elastic/elasticsearch/issues/117745
+- class: org.elasticsearch.xpack.esql.ccq.MultiClusterSpecIT
+  method: test {scoring.QstrWithFieldAndScoringSortedEval}
+  issue: https://github.com/elastic/elasticsearch/issues/117751
+- class: org.elasticsearch.search.ccs.CrossClusterIT
+  method: testCancel
+  issue: https://github.com/elastic/elasticsearch/issues/108061
+- class: org.elasticsearch.test.rest.yaml.CcsCommonYamlTestSuiteIT
+  method: test {p0=search.highlight/50_synthetic_source/text multi unified from vectors}
+  issue: https://github.com/elastic/elasticsearch/issues/117815
+- class: org.elasticsearch.xpack.ml.integration.DatafeedJobsRestIT
+  issue: https://github.com/elastic/elasticsearch/issues/111319
+- class: org.elasticsearch.validation.DotPrefixClientYamlTestSuiteIT
+  issue: https://github.com/elastic/elasticsearch/issues/117893
+- class: org.elasticsearch.xpack.core.ml.search.SparseVectorQueryBuilderTests
+  method: testToQuery
+  issue: https://github.com/elastic/elasticsearch/issues/117904
+- class: org.elasticsearch.packaging.test.ArchiveGenerateInitialCredentialsTests
+  method: test20NoAutoGenerationWhenAutoConfigurationDisabled
+  issue: https://github.com/elastic/elasticsearch/issues/117891
+- class: org.elasticsearch.packaging.test.BootstrapCheckTests
+  method: test20RunWithBootstrapChecks
+  issue: https://github.com/elastic/elasticsearch/issues/117890
+- class: org.elasticsearch.xpack.esql.plugin.ClusterRequestTests
+  method: testFallbackIndicesOptions
+  issue: https://github.com/elastic/elasticsearch/issues/117937
+- class: org.elasticsearch.xpack.esql.qa.single_node.RequestIndexFilteringIT
+  method: testFieldExistsFilter_KeepWildcard
+  issue: https://github.com/elastic/elasticsearch/issues/117935
+- class: org.elasticsearch.xpack.esql.qa.multi_node.RequestIndexFilteringIT
+  method: testFieldExistsFilter_KeepWildcard
+  issue: https://github.com/elastic/elasticsearch/issues/117935
+- class: org.elasticsearch.xpack.ml.integration.RegressionIT
+  method: testTwoJobsWithSameRandomizeSeedUseSameTrainingSet
+  issue: https://github.com/elastic/elasticsearch/issues/117805
 
 # Examples:
 #
@@ -386,31 +283,3 @@ tests:
 #  - class: "org.elasticsearch.xpack.esql.**"
 #    method: "test {union_types.MultiIndexIpStringStatsInline *}"
 #    issue: "https://github.com/elastic/elasticsearch/..."
-- class: org.elasticsearch.reservedstate.service.FileSettingsServiceTests
-  method: testStopWorksInMiddleOfProcessing
-  issue: https://github.com/elastic/elasticsearch/issues/117591
-- class: org.elasticsearch.repositories.s3.RepositoryS3ClientYamlTestSuiteIT
-  issue: https://github.com/elastic/elasticsearch/issues/117596
-- class: "org.elasticsearch.xpack.esql.qa.multi_node.EsqlSpecIT"
-  method: "test {scoring.*}"
-  issue: https://github.com/elastic/elasticsearch/issues/117641
-- class: "org.elasticsearch.xpack.esql.qa.single_node.EsqlSpecIT"
-  method: "test {scoring.*}"
-  issue: https://github.com/elastic/elasticsearch/issues/117641
-- class: "org.elasticsearch.xpack.esql.qa.mixed.MixedClusterEsqlSpecIT"
-  method: "test {scoring.*}"
-  issue: https://github.com/elastic/elasticsearch/issues/117641
-- class: org.elasticsearch.xpack.esql.ccq.MultiClusterSpecIT
-  method: test {scoring.QstrWithFieldAndScoringSortedEval}
-  issue: https://github.com/elastic/elasticsearch/issues/117751
-- class: org.elasticsearch.search.ccs.CrossClusterIT
-  method: testCancel
-  issue: https://github.com/elastic/elasticsearch/issues/108061
-- class: org.elasticsearch.xpack.ml.integration.RegressionIT
-  method: testTwoJobsWithSameRandomizeSeedUseSameTrainingSet
-  issue: https://github.com/elastic/elasticsearch/issues/117805
-- class: org.elasticsearch.xpack.test.rest.XPackRestIT
-  method: test {p0=esql/60_usage/Basic ESQL usage output (telemetry) non-snapshot version}
-  issue: https://github.com/elastic/elasticsearch/issues/117862
-- class: org.elasticsearch.xpack.security.authc.ldap.UserAttributeGroupsResolverTests
-  issue: https://github.com/elastic/elasticsearch/issues/116537
diff --git a/test/framework/src/main/java/org/elasticsearch/test/rest/ESRestTestCase.java b/test/framework/src/main/java/org/elasticsearch/test/rest/ESRestTestCase.java
index 40703e7b6bada..359fbdf7d0220 100644
--- a/test/framework/src/main/java/org/elasticsearch/test/rest/ESRestTestCase.java
+++ b/test/framework/src/main/java/org/elasticsearch/test/rest/ESRestTestCase.java
@@ -26,6 +26,8 @@
 import org.apache.http.ssl.SSLContextBuilder;
 import org.apache.http.ssl.SSLContexts;
 import org.apache.http.util.EntityUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.elasticsearch.Build;
 import org.elasticsearch.TransportVersion;
 import org.elasticsearch.TransportVersions;
@@ -158,6 +160,8 @@ public abstract class ESRestTestCase extends ESTestCase {
 
     private static final Pattern SEMANTIC_VERSION_PATTERN = Pattern.compile("^(\\d+\\.\\d+\\.\\d+)\\D?.*");
 
+    private static final Logger SUITE_LOGGER = LogManager.getLogger(ESRestTestCase.class);
+
     /**
      * Convert the entity from a {@link Response} into a map of maps.
      * Consumes the underlying HttpEntity, releasing any resources it may be holding.
@@ -1171,7 +1175,13 @@ protected static void wipeAllIndices(boolean preserveSecurityIndices) throws IOE
             }
             final Request deleteRequest = new Request("DELETE", Strings.collectionToCommaDelimitedString(indexPatterns));
             deleteRequest.addParameter("expand_wildcards", "open,closed" + (includeHidden ? ",hidden" : ""));
-            deleteRequest.setOptions(deleteRequest.getOptions().toBuilder().setWarningsHandler(ignoreAsyncSearchWarning()).build());
+
+            // If system index warning, ignore but log
+            // See: https://github.com/elastic/elasticsearch/issues/117099
+            // and: https://github.com/elastic/elasticsearch/issues/115809
+            deleteRequest.setOptions(
+                RequestOptions.DEFAULT.toBuilder().setWarningsHandler(ESRestTestCase::ignoreSystemIndexAccessWarnings)
+            );
             final Response response = adminClient().performRequest(deleteRequest);
             try (InputStream is = response.getEntity().getContent()) {
                 assertTrue((boolean) XContentHelper.convertToMap(XContentType.JSON.xContent(), is, true).get("acknowledged"));
@@ -1184,28 +1194,16 @@ protected static void wipeAllIndices(boolean preserveSecurityIndices) throws IOE
         }
     }
 
-    // Make warnings handler that ignores the .async-search warning since .async-search may randomly appear when async requests are slow
-    // See: https://github.com/elastic/elasticsearch/issues/117099
-    protected static WarningsHandler ignoreAsyncSearchWarning() {
-        return new WarningsHandler() {
-            @Override
-            public boolean warningsShouldFailRequest(List<String> warnings) {
-                if (warnings.isEmpty()) {
-                    return false;
-                }
-                return warnings.equals(
-                    List.of(
-                        "this request accesses system indices: [.async-search], "
-                            + "but in a future major version, direct access to system indices will be prevented by default"
-                    )
-                ) == false;
+    private static boolean ignoreSystemIndexAccessWarnings(List<String> warnings) {
+        for (String warning : warnings) {
+            if (warning.startsWith("this request accesses system indices:")) {
+                SUITE_LOGGER.warn("Ignoring system index access warning during test cleanup: {}", warning);
+            } else {
+                return true;
             }
+        }
 
-            @Override
-            public String toString() {
-                return "ignore .async-search warning";
-            }
-        };
+        return false;
     }
 
     protected static void wipeDataStreams() throws IOException {