diff --git a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/controller/StandardFlowSynchronizer.java b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/controller/StandardFlowSynchronizer.java
index 9bb3d2f565..425110c527 100644
--- a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/controller/StandardFlowSynchronizer.java
+++ b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/controller/StandardFlowSynchronizer.java
@@ -240,7 +240,7 @@ public class StandardFlowSynchronizer implements FlowSynchronizer {
                     existingFlowEmpty = taskElements.isEmpty()
                         && unrootedControllerServiceElements.isEmpty()
                         && isEmpty(rootGroupDto)
-                        && registriesPresent;
+                        && !registriesPresent;
                     logger.debug("Existing Flow Empty = {}", existingFlowEmpty);
                 }
             }
diff --git a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/groups/StandardProcessGroup.java b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/groups/StandardProcessGroup.java
index 870804d52a..9418f40852 100644
--- a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/groups/StandardProcessGroup.java
+++ b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-framework-core/src/main/java/org/apache/nifi/groups/StandardProcessGroup.java
@@ -3316,7 +3316,17 @@ public final class StandardProcessGroup implements ProcessGroup {
             ancestorServiceIds = Collections.emptySet();
         } else {
             ancestorServiceIds = parentGroup.getControllerServices(true).stream()
-                .map(ControllerServiceNode::getIdentifier)
+                .map(cs -> {
+                    // We want to map the Controller Service to its Versioned Component ID, if it has one.
+                    // If it does not have one, we want to generate it in the same way that our Flow Mapper does
+                    // because this allows us to find the Controller Service when doing a Flow Diff.
+                    final Optional<String> versionedId = cs.getVersionedComponentId();
+                    if (versionedId.isPresent()) {
+                        return versionedId.get();
+                    }
+
+                    return UUID.nameUUIDFromBytes(cs.getIdentifier().getBytes(StandardCharsets.UTF_8)).toString();
+                })
                 .collect(Collectors.toSet());
         }
 
diff --git a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-web/nifi-web-api/src/main/java/org/apache/nifi/web/StandardNiFiServiceFacade.java b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-web/nifi-web-api/src/main/java/org/apache/nifi/web/StandardNiFiServiceFacade.java
index b7559ec573..1ccced2f1e 100644
--- a/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-web/nifi-web-api/src/main/java/org/apache/nifi/web/StandardNiFiServiceFacade.java
+++ b/nifi-nar-bundles/nifi-framework-bundle/nifi-framework/nifi-web/nifi-web-api/src/main/java/org/apache/nifi/web/StandardNiFiServiceFacade.java
@@ -3824,7 +3824,17 @@ public class StandardNiFiServiceFacade implements NiFiServiceFacade {
             ancestorServiceIds = Collections.emptySet();
         } else {
             ancestorServiceIds = parentGroup.getControllerServices(true).stream()
-                .map(ControllerServiceNode::getIdentifier)
+                .map(cs -> {
+                    // We want to map the Controller Service to its Versioned Component ID, if it has one.
+                    // If it does not have one, we want to generate it in the same way that our Flow Mapper does
+                    // because this allows us to find the Controller Service when doing a Flow Diff.
+                    final Optional<String> versionedId = cs.getVersionedComponentId();
+                    if (versionedId.isPresent()) {
+                        return versionedId.get();
+                    }
+
+                    return UUID.nameUUIDFromBytes(cs.getIdentifier().getBytes(StandardCharsets.UTF_8)).toString();
+                })
                 .collect(Collectors.toSet());
         }