Replacing a prefab with a new one to update model changes

Hi all! I've been trying to solve a problem we have with prefabs for some days without success so I feel it's time to ask the community for ideas. We have the situation where we have several objects on a scene instantiated from a prefab that was created using a model asset from the repository. On this prefab several components were added. Later the model has to be changed and several additional bones were added to it. This brokes down the mesh on the game. So we must update the prefab to get the changes on the model. Dragging and dropping the model asset again into the prefab works but it makes all the components the prefab has to be lost. To avoid this I have come to a semi automated solution using scripting. Here's the code:

         GameObject tempInstance = GameObject.Instantiate(model) as GameObject;

         GameObject newInstance = EditorUtility.InstantiatePrefab(oldPrefab) as GameObject;

         Component[] fromComps = newInstance.GetComponents(typeof(Component));

         foreach(Component c in fromComps)

         {

             Component nc = tempInstance.GetComponent(c.GetType());

             if( nc == null)

                 nc = tempInstance.AddComponent(c.GetType());

             foreach (FieldInfo f in c.GetType().GetFields())

             {

               f.SetValue(nc, f.GetValue(c));

             }

             foreach (PropertyInfo p in c.GetType().GetProperties())

             {

                 if(p.CanWrite && p.CanRead)

                     p.SetValue(nc, p.GetValue(c,null),null);

             }

         }

         EditorUtility.ReplacePrefab(tempInstance,oldPrefab);

         AssetDatabase.Refresh();
 
         GameObject.DestroyImmediate(tempInstance);

         GameObject.DestroyImmediate(newInstance);
 

Where 'model' is a reference to the source model asset in the library and 'oldPrefab' is a reference to the prefab object that we want to update.

The problem is that when I call 'ReplacePrefab' it seems that all the instances that were created from the old prefab are deleted and created again, so all the references that I had to these objects in other objects of the scene are lost. In fact, the call to DestroyImmediate(newInstance) gives an error that I'm trying to access an object that has already been destroyed. I don't know how to avoid all the instances to be 'recreated' when updating the prefab, neither I know if this is possible.

Other solution would be to create the prefabs not using the model asset directly, but using an empty game object and then adding the model as a child of it. But this solution would mean that I must change a lot of script code for the components (they must acces the model or the animation component one level deeper in the hierarchy) and also to make again all the scenes, which is a lot of work at this point of development.

¿Any help?