diff --git a/openpype/settings/entities/dict_immutable_keys_entity.py b/openpype/settings/entities/dict_immutable_keys_entity.py
index cdb3b9aebe..2f69a40d45 100644
--- a/openpype/settings/entities/dict_immutable_keys_entity.py
+++ b/openpype/settings/entities/dict_immutable_keys_entity.py
@@ -356,10 +356,15 @@ class DictImmutableKeysEntity(ItemEntity):
 
         old_metadata = metadata.get(M_OVERRIDEN_KEY)
         if old_metadata:
+            old_metadata_set = set(old_metadata)
             new_metadata = []
             for key in self.non_gui_children.keys():
                 if key in old_metadata:
                     new_metadata.append(key)
+                    old_metadata_set.remove(key)
+
+            for key in old_metadata_set:
+                new_metadata.append(key)
             metadata[M_OVERRIDEN_KEY] = new_metadata
 
         return value, metadata