Via script Inspector changed variable is default on build (like prefab)

Code (CSharp):

1.  
2. [InitializeOnLoad]
3. public static class NetworkSceneObjectEditor
4. {
5.  
6.     static NetworkSceneObjectEditor()
7.     {
8.         if(!EditorApplication.isPlaying)
9.             EditorApplication.hierarchyChanged += OnHierarchyChanged;
10.     }
11.  
12.     static void OnHierarchyChanged()
13.     {
14.         if (EditorApplication.isPlaying)
15.             return;
16.  
17.         var all = Resources.FindObjectsOfTypeAll<NetworkSceneObject>();
18.         var networkSceneObjects = all.Where(obj => (obj.hideFlags & HideFlags.HideInHierarchy) != HideFlags.HideInHierarchy);
19.         //Debug.LogFormat("There are currently {0} GameObjects visible in the hierarchy.", networkSceneObjects.Count());
20.  
21.         int i = 0;
22.         foreach (var o in networkSceneObjects)
23.         {
24.             var netObject = o.GetComponent<NetworkObject>();
25.             if (netObject == null)
26.             {
27.                 Debug.Log("NetworkObject is missing! NetworkSceneObject will not work");
28.                 continue;
29.             }
30.  
31.             o.scenenNetId = i;
32.             netObject.NetId = i;
33.  
34.             //Debug.Log($"{netObject.gameObject.name} {i}");
35.             i++;
36.         }
37.     }
38. }
39.  

With this script properties get changed if something is changed in the hierarchy like duplicating or adding new gameobjects. It is just increasing the id number.

I have two problems here.
1. If I am in playmode and I change to the scene with those gameObjects sometimes the values are reseted to the value which I edit myself in the inspector.
2. If I make build version.. the ideas will be reseted to default value of the prefab (to 0).

So I think I am missing there something like "Save this objects" or "Save this edit".

Any ideas?