How can I destroy an object that is in a prefab and part of the prefab ?

Code (csharp):

1.  
2. using System.Collections;
3. using System.Collections.Generic;
4. using System.Linq;
5. using UnityEditor;
6. using UnityEngine;
7.  
8. public class ObjectsReplace : MonoBehaviour
9. {
10.     public GameObject prefabToInit;
11.  
12.     // Note your method should probably return something
13.     public void UpdateOrAddShaderPrefabToDoors()
14.     {
15.         GameObject[] doorsLeft = GameObject.FindGameObjectsWithTag("Door_Left");
16.         GameObject[] doorsRight = GameObject.FindGameObjectsWithTag("Door_Right");
17.  
18.         List<GameObject> allDoors = doorsLeft.Union(doorsRight).ToList();
19.  
20.         allDoors.ForEach(gameObject =>
21.         {
22.             Transform childTransform = gameObject.transform.Find("DoorShieldFXLocked Variant");
23.             GameObject child = childTransform?.gameObject;
24.             Debug.Log($"Child exist: {child != null}, Name of child: {child?.name}");
25.             if (child != null)
26.             {
27.                 //ModifyPrefab(child);
28.             }
29.         });
30.     }
31.  
32.     private void ModifyPrefab(GameObject child)
33.     {
34.         var mostPrefabInstanceRoot = PrefabUtility.GetOutermostPrefabInstanceRoot(child);
35.  
36.         // Get the Prefab Asset root GameObject and its asset path.
37.         string assetPath = PrefabUtility.GetPrefabAssetPathOfNearestInstanceRoot(mostPrefabInstanceRoot);
38.  
39.         // Load the contents of the Prefab Asset.
40.         GameObject contentsRoot = PrefabUtility.LoadPrefabContents(assetPath);
41.  
42.         // Modify Prefab contents.
43.         DestroyImmediate(child);
44.  
45.         // Save contents back to Prefab Asset and unload contents.
46.         PrefabUtility.SaveAsPrefabAsset(mostPrefabInstanceRoot, assetPath);
47.         PrefabUtility.UnloadPrefabContents(mostPrefabInstanceRoot);
48.     }
49. }
50.  

I'm trying to do the same in the editor : Overrides > Apply Changes

But I'm still getting exception in the console on the line :

Code (csharp):

1.  
2. DestroyImmediate(child);
3.  

You can't destroy object that is part of prefab.

Another problem is in one of my tests when changing the code it's changed the prefabs to regular objects.
Lucky I did a backup but not sure why it's changed the prefabs in the hierarchy to regular gameobjects.