diff --git a/x-pack/plugins/ingest_manager/server/services/agent_config.ts b/x-pack/plugins/ingest_manager/server/services/agent_config.ts
index 0a9adc1f1c593..3886146e28806 100644
--- a/x-pack/plugins/ingest_manager/server/services/agent_config.ts
+++ b/x-pack/plugins/ingest_manager/server/services/agent_config.ts
@@ -233,16 +233,14 @@ class AgentConfigService {
     if (baseAgentConfig.package_configs.length) {
       const newPackageConfigs = (baseAgentConfig.package_configs as PackageConfig[]).map(
         (packageConfig: PackageConfig) => {
-          const { id: packageConfigId, ...newPackageConfig } = packageConfig;
+          const { id: packageConfigId, version, ...newPackageConfig } = packageConfig;
           return newPackageConfig;
         }
       );
-      await packageConfigService.bulkCreate(
-        soClient,
-        newPackageConfigs,
-        newAgentConfig.id,
-        options
-      );
+      await packageConfigService.bulkCreate(soClient, newPackageConfigs, newAgentConfig.id, {
+        ...options,
+        bumpConfigRevision: false,
+      });
     }
 
     // Get updated config
diff --git a/x-pack/plugins/ingest_manager/server/services/package_config.ts b/x-pack/plugins/ingest_manager/server/services/package_config.ts
index c2d465cf7c73f..5d1c5d1717714 100644
--- a/x-pack/plugins/ingest_manager/server/services/package_config.ts
+++ b/x-pack/plugins/ingest_manager/server/services/package_config.ts
@@ -121,7 +121,7 @@ class PackageConfigService {
     options?: { user?: AuthenticatedUser; bumpConfigRevision?: boolean }
   ): Promise<PackageConfig[]> {
     const isoDate = new Date().toISOString();
-    const { saved_objects: newSos } = await soClient.bulkCreate<PackageConfigSOAttributes>(
+    const { saved_objects } = await soClient.bulkCreate<PackageConfigSOAttributes>(
       packageConfigs.map((packageConfig) => ({
         type: SAVED_OBJECT_TYPE,
         attributes: {
@@ -136,6 +136,9 @@ class PackageConfigService {
       }))
     );
 
+    // Filter out invalid SOs
+    const newSos = saved_objects.filter((so) => !so.error && so.attributes);
+
     // Assign it to the given agent config
     await agentConfigService.assignPackageConfigs(
       soClient,