How to make my scene object reference survive the button play

Hi,

I did the tour of Google and Unity resources, I just can't seem to find an answer to my problem.

Basically I want use an EditorWindow to generate and manipulate some graphs tree that are then evaluated during the game. I generate those trees in the scene directly I may sometimes save them separately into a prefab but most of the time I just keep them into the scenes.

My drama as a lot of people had starts when I click play. The evaluation of the tree happens correctly but the visual of the tree I had in my custom editor window just vanished because it loses the reference to the scene object. So if I want to have this visual I need to redo the link manually on play time which is annoying.

Here is a sample to illustrate the same issue I basically have:

 [System.Serializable]
 public class Data : MonoBehaviour
 {
     public int difficulty = 0;
     public string description;
 }
 
 public class MyWindow : EditorWindow 
 {
     [SerializeField] // To be sure it is serialized
     public Data data;
 
     // Add menu named "My Window" to the Window menu
     [MenuItem ("Window/My Window")]
     static void Init () 
     {
         // Get existing open window or if none, make a new one:
         MyWindow window = (MyWindow)EditorWindow.GetWindow (typeof (MyWindow));
         window.Show();
     }
 
     void OnEnable()
     {
         hideFlags = HideFlags.HideAndDontSave; // Tried that
         EditorUtility.SetDirty(data); // that too
     }
 
     void OnGUI () 
     {
         data = (Data)EditorGUILayout.ObjectField(data, typeof(Data), true);
     }
 }

And here is my scene, where GameObject have Data attached to it and GameObject (1).

Whichever the one I use, the ObjectField keeps getting reset on play. While if I use the prefab of GameObject in the project panel it doesn't. But it isn't the prefab that will be running in my scene and that I want to debug. It's the real instance in the scene...

Am I trying to do something that cannot be done?

Thanks.