diff --git a/muted-tests.yml b/muted-tests.yml
index 186b2f2b8b90a..79c916d9a348e 100644
--- a/muted-tests.yml
+++ b/muted-tests.yml
@@ -66,9 +66,6 @@ tests:
 - 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.xpack.deprecation.DeprecationHttpIT
-  method: testDeprecatedSettingsReturnWarnings
-  issue: https://github.com/elastic/elasticsearch/issues/108628
 - class: org.elasticsearch.xpack.shutdown.NodeShutdownIT
   method: testAllocationPreventedForRemoval
   issue: https://github.com/elastic/elasticsearch/issues/116363
diff --git a/server/src/main/java/org/elasticsearch/cluster/service/MasterService.java b/server/src/main/java/org/elasticsearch/cluster/service/MasterService.java
index c46b3b7d66183..05fa03283d065 100644
--- a/server/src/main/java/org/elasticsearch/cluster/service/MasterService.java
+++ b/server/src/main/java/org/elasticsearch/cluster/service/MasterService.java
@@ -913,7 +913,7 @@ public void onFailure(Exception failure) {
 
         @Override
         public Releasable captureResponseHeaders() {
-            final var storedContext = threadContext.newStoredContext();
+            final var storedContext = threadContextSupplier.get();
             return Releasables.wrap(() -> {
                 final var newResponseHeaders = threadContext.getResponseHeaders();
                 if (newResponseHeaders.isEmpty()) {
diff --git a/server/src/test/java/org/elasticsearch/cluster/service/MasterServiceTests.java b/server/src/test/java/org/elasticsearch/cluster/service/MasterServiceTests.java
index 0fecccc3cb5e6..4c24abbd5fd9a 100644
--- a/server/src/test/java/org/elasticsearch/cluster/service/MasterServiceTests.java
+++ b/server/src/test/java/org/elasticsearch/cluster/service/MasterServiceTests.java
@@ -299,7 +299,6 @@ public void testThreadContext() {
             }
 
             try (ThreadContext.StoredContext ignored = threadPool.getThreadContext().stashContext()) {
-
                 final var expectedHeaders = new HashMap<String, String>();
                 expectedHeaders.put(randomIdentifier(), randomIdentifier());
                 for (final var copiedHeader : Task.HEADERS_TO_COPY) {
@@ -319,8 +318,10 @@ public void testThreadContext() {
                     new AckedClusterStateUpdateTask(ackedRequest(ackTimeout, masterTimeout), null) {
                         @Override
                         public ClusterState execute(ClusterState currentState) {
-                            assertTrue(threadPool.getThreadContext().isSystemContext());
-                            assertEquals(Collections.emptyMap(), threadPool.getThreadContext().getHeaders());
+                            // the task is executed in the context in which the task was originally created.
+                            // note: this is typically not a system context.
+                            assertExpectedThreadContext(Map.of());
+
                             expectedResponseHeaders.forEach(
                                 (name, values) -> values.forEach(v -> threadPool.getThreadContext().addResponseHeader(name, v))
                             );
diff --git a/x-pack/plugin/build.gradle b/x-pack/plugin/build.gradle
index 7adcf50a256e2..7605c8060f873 100644
--- a/x-pack/plugin/build.gradle
+++ b/x-pack/plugin/build.gradle
@@ -105,7 +105,11 @@ tasks.named("yamlRestCompatTestTransform").configure({ task ->
   task.skipTest("esql/130_spatial/values unsupported for geo_point", "Spatial types are now supported in VALUES aggregation")
   task.skipTest("esql/130_spatial/values unsupported for geo_point status code", "Spatial types are now supported in VALUES aggregation")
   // Expected deprecation warning to compat yaml tests:
-  task.addAllowedWarningRegex(".*rollup functionality will be removed in Elasticsearch.*")
+  task.addAllowedWarningRegex(
+    ".*rollup functionality will be removed in Elasticsearch.*",
+    // https://github.com/elastic/elasticsearch/issues/127911
+    "Index \\[\\.profiling-.*\\] name begins with a dot.* and will not be allowed in a future Elasticsearch version."
+  )
   task.skipTest("esql/40_tsdb/from doc with aggregate_metric_double", "TODO: support for subset of metric fields")
   task.skipTest("esql/40_tsdb/stats on aggregate_metric_double", "TODO: support for subset of metric fields")
   task.skipTest("esql/40_tsdb/from index pattern unsupported counter", "TODO: support for subset of metric fields")
diff --git a/x-pack/plugin/src/yamlRestTest/resources/rest-api-spec/test/profiling/10_basic.yml b/x-pack/plugin/src/yamlRestTest/resources/rest-api-spec/test/profiling/10_basic.yml
index 9996f67c4ecb6..f026bcebc2a09 100644
--- a/x-pack/plugin/src/yamlRestTest/resources/rest-api-spec/test/profiling/10_basic.yml
+++ b/x-pack/plugin/src/yamlRestTest/resources/rest-api-spec/test/profiling/10_basic.yml
@@ -1,10 +1,14 @@
 ---
 setup:
   - requires:
+      test_runner_features: [ "allowed_warnings_regex" ]
       cluster_features: ["gte_v8.13.0"]
       reason: "Universal Profiling test infrastructure is available in 8.12+"
 
   - do:
+      allowed_warnings_regex:
+        # https://github.com/elastic/elasticsearch/issues/127911
+        - "Index \\[\\.profiling-.*\\] name begins with a dot .* and will not be allowed in a future Elasticsearch version."
       cluster.put_settings:
         body:
           persistent: