Prefab is "forgetting" public variables on instantiation

Hello, I have a problem where I can't find a solution:

I'm adding objects to a list on a script on a prefab with this code:

Code (CSharp):

1.         if (UnityEditor.Experimental.SceneManagement.PrefabStageUtility.GetCurrentPrefabStage() != null) // In Prefab Mode
2.         {
3.             RoomConfig currentConfig = UnityEditor.Experimental.SceneManagement.PrefabStageUtility.GetCurrentPrefabStage().FindComponentOfType<RoomConfig>();
4.             string path = UnityEditor.Experimental.SceneManagement.PrefabStageUtility.GetPrefabStage(Selection.activeObject as
5.                  GameObject).assetPath; // Get the prefab path in disk
6.             GameObject prefabRoot = PrefabUtility.LoadPrefabContents(path); // Load the contents of the prefab.
7.             SerializedObject saveConfig = new SerializedObject(currentConfig);
8.             currentConfig.AddPositionMarker(this); // Add a reference to this object to the RoomConfig
9.  
10.             saveConfig.Update();
11.             saveConfig.ApplyModifiedProperties();// Apply after editing so that the values are stored
12.  
13.             try
14.             {
15.                 PrefabUtility.SaveAsPrefabAsset(prefabRoot, path); // Save the prefab to disk    
16.                 Debug.Log("Saving prefab");
17.             }
18.              finally
19.             {
20.                 PrefabUtility.UnloadPrefabContents(prefabRoot);     // Unload to clear memory..              
21.             }
22.         }
23.         else
24.         {
25.             RoomConfig currentConfig = FindObjectOfType<RoomConfig>();
26.             currentConfig.AddPositionMarker(this);
27.             EditorUtility.SetDirty(currentConfig);
28.         }

Now this works fine in the Prefab Editor. I can see the added reference in the public field of the RoomConfig. (Yes I made sure it's public and gets saved ^^)

However when I instatiate the Prefab during Runtime I have this weird behaviour:
It works the first time just fine. But when I start the Scene a second time the Prefab loses the added references.

When I drag the prefab into the current scene the added fields get automatically flagged as "changed" by the Editor. (Bold font and listed in the override list).

What am I doing wrong? Or is it a bug?

 

Ok, found the answer myself. I needed to add the "EditorUtility.SetDirty" also to the Prefab Editor branch.