diff --git a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/persistence/IndexBasedTransformConfigManager.java b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/persistence/IndexBasedTransformConfigManager.java
index 25630fb24772a..360ef28c9815c 100644
--- a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/persistence/IndexBasedTransformConfigManager.java
+++ b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/persistence/IndexBasedTransformConfigManager.java
@@ -295,16 +295,19 @@ public void deleteOldIndices(ActionListener<Boolean> listener) {
 
         // use the transform context as we access system indexes
         try (ThreadContext.StoredContext ctx = client.threadPool().getThreadContext().stashWithOrigin(TRANSFORM_ORIGIN)) {
-            indicesToDelete.addAll(
-                Arrays.asList(
-                    indexNameExpressionResolver.concreteIndexNames(
-                        state,
-                        IndicesOptions.lenientExpandHidden(),
-                        TransformInternalIndexConstants.INDEX_NAME_PATTERN
-                    )
-                )
+            var matchingIndexes = indexNameExpressionResolver.concreteIndices(
+                state,
+                IndicesOptions.lenientExpandHidden(),
+                TransformInternalIndexConstants.INDEX_NAME_PATTERN
             );
 
+            for (var index : matchingIndexes) {
+                var meta = state.getMetadata().getIndexSafe(index);
+                if (meta.isSystem() == false) { // ignore system indices as these are automatically managed
+                    indicesToDelete.add(meta.getIndex().getName());
+                }
+            }
+
             indicesToDelete.addAll(
                 Arrays.asList(
                     indexNameExpressionResolver.concreteIndexNames(
diff --git a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MLModelDeploymentsUpgradeIT.java b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MLModelDeploymentsUpgradeIT.java
index 83ea9071eca90..7f486266c1a7f 100644
--- a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MLModelDeploymentsUpgradeIT.java
+++ b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MLModelDeploymentsUpgradeIT.java
@@ -72,10 +72,10 @@ public void setUpLogging() throws IOException {
         request.setJsonEntity("""
             {
               "persistent": {
-                "logger.org.elasticsearch.xpack.ml.inference": "TRACE",
+                "logger.org.elasticsearch.xpack.ml.inference": "DEBUG",
                 "logger.org.elasticsearch.xpack.ml.inference.assignments": "DEBUG",
                 "logger.org.elasticsearch.xpack.ml.process": "DEBUG",
-                "logger.org.elasticsearch.xpack.ml.action": "TRACE"
+                "logger.org.elasticsearch.xpack.ml.action": "DEBUG"
               }
             }
             """);
diff --git a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/TransformSurvivesUpgradeIT.java b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/TransformSurvivesUpgradeIT.java
index 87a9911bd80b6..ab26223bce387 100644
--- a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/TransformSurvivesUpgradeIT.java
+++ b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/TransformSurvivesUpgradeIT.java
@@ -35,7 +35,6 @@
 import static org.elasticsearch.xpack.test.rest.XPackRestTestConstants.TRANSFORM_INTERNAL_INDEX_PREFIX;
 import static org.elasticsearch.xpack.test.rest.XPackRestTestConstants.TRANSFORM_INTERNAL_INDEX_PREFIX_DEPRECATED;
 import static org.elasticsearch.xpack.test.rest.XPackRestTestConstants.TRANSFORM_TASK_NAME;
-import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.greaterThanOrEqualTo;
@@ -96,7 +95,6 @@ public void testTransformRollingUpgrade() throws Exception {
                     lastCheckpoint = 2;
                 }
                 verifyContinuousTransformHandlesData(lastCheckpoint);
-                verifyUpgradeFailsIfMixedCluster();
             }
             case UPGRADED -> {
                 client().performRequest(waitForYellow);
@@ -131,11 +129,11 @@ private void createAndStartContinuousTransform() throws Exception {
 
         assertBusy(() -> {
             var stateAndStats = getTransformStats(CONTINUOUS_TRANSFORM_ID);
+            assertThat((Integer) XContentMapValues.extractValue("stats.documents_indexed", stateAndStats), equalTo(ENTITIES.size()));
             assertThat(
-                ((Integer) XContentMapValues.extractValue("stats.documents_indexed", stateAndStats)).longValue(),
-                equalTo(ENTITIES.size())
+                ((Integer) XContentMapValues.extractValue("stats.documents_processed", stateAndStats)).longValue(),
+                equalTo(totalDocsWritten)
             );
-            assertThat((Integer) XContentMapValues.extractValue("stats.documents_processed", stateAndStats), equalTo(totalDocsWritten));
             // Even if we get back to started, we may periodically get set back to `indexing` when triggered.
             // Though short lived due to no changes on the source indices, it could result in flaky test behavior
             assertThat(stateAndStats.get("state"), oneOf("started", "indexing"));
@@ -232,17 +230,6 @@ private void verifyContinuousTransformHandlesData(long expectedLastCheckpoint) t
         });
     }
 
-    private void verifyUpgradeFailsIfMixedCluster() {
-        // upgrade tests by design are also executed with the same version, this check must be skipped in this case, see gh#39102.
-        if (isOriginalClusterCurrent()) {
-            return;
-        }
-        final Request upgradeTransformRequest = new Request("POST", getTransformEndpoint() + "_upgrade");
-
-        Exception ex = expectThrows(Exception.class, () -> client().performRequest(upgradeTransformRequest));
-        assertThat(ex.getMessage(), containsString("All nodes must be the same version"));
-    }
-
     private void verifyUpgrade() throws IOException {
         final Request upgradeTransformRequest = new Request("POST", getTransformEndpoint() + "_upgrade");
         Response response = client().performRequest(upgradeTransformRequest);