diff --git a/.github/workflows/complete-e2e.yml b/.github/workflows/complete-e2e.yml
index 4e06ce371..d27eb0018 100644
--- a/.github/workflows/complete-e2e.yml
+++ b/.github/workflows/complete-e2e.yml
@@ -67,7 +67,9 @@ jobs:
           {zip: "fileSingleRoot.zip", name: "fileSingleRoot", folder: "fileSingleRoot", language: "java", cliArgs: ""},
           {zip: "folderSingleRoot.zip", name: "folderSingleRoot", folder: "folderSingleRoot", language: "java", cliArgs: ""},
           {zip: "fileMultiRoot.zip", name: "fileMultiRoot", folder: "f0", language: "java", cliArgs: "--new f1"},
-          {zip: "folderMultiRoot.zip", name: "folderMultiRoot", folder: "f0", language: "java", cliArgs: "--new f1"}
+          {zip: "folderMultiRoot.zip", name: "folderMultiRoot", folder: "f0", language: "java", cliArgs: "--new f1"},
+          {zip: "mixedMultiRoot.zip", name: "mixedBaseFile", folder: "f0", language: "java", cliArgs: "--new f1"},
+          {zip: "mixedMultiRoot.zip", name: "mixedBaseFolder", folder: "f1", language: "java", cliArgs: "--new f0"}
           ]
 
     steps:
diff --git a/report-viewer/tests/e2e/OpenComparisonTest.spec.ts b/report-viewer/tests/e2e/OpenComparisonTest.spec.ts
index a0fe30be3..5a3976e7c 100644
--- a/report-viewer/tests/e2e/OpenComparisonTest.spec.ts
+++ b/report-viewer/tests/e2e/OpenComparisonTest.spec.ts
@@ -24,6 +24,16 @@ const testSets: DataSet[] = [
     datasetName: 'fileMultiRoot-report.zip',
     firstSubmissionName: 'f0\\\\|/0.java',
     secondSubmissionName: 'f1\\\\|/1.java'
+  },
+  {
+    datasetName: 'mixedBaseFile-report.zip',
+    firstSubmissionName: 'f0\\\\|/0.java',
+    secondSubmissionName: 'f1\\\\|/1'
+  },
+  {
+    datasetName: 'mixedBaseFolder-report.zip',
+    firstSubmissionName: 'f0\\\\|/0.java',
+    secondSubmissionName: 'f1\\\\|/1'
   },*/
   {
     datasetName: 'folderMultiRoot-report.zip',