Referencing a prefab in another prefab created programmatically

Howdy,

I'm currently trying to streamline part of my workflow of creating a slightly altered duplicate of a number of prefabs. The prefabs i have created manually contain a structure component script with an enum along with a few transforms as shown below:

I also have a 'structure component silhouette' script which should reference it's corresponding structure component

Via a button added in an editor script in a separate gameobject, a script grabs all prefabs in a given directory, and for each prefab does the following:

1. instantiate a copy of the prefab

2. remove the structure component script

3. add a 'Structure component silhouette' script

4. Set the pivots of the silhouette script (working)

5. Set the Comp reference to be the source prefab GameObject (not working)

6. Save the new object to a given directory (working)

   ---

The essence of my question is, what am i doing wrong here, i could go and drag and drop the existing structure component prefab into the new silhouette prefab, but i cannot seem to get it to stick programmatically. Code for this process shown below:

 public class StructureComponentGenerator : MonoBehaviour
 {
     private List<GameObject> SilhouettesToCreate;
     public string LoadFromPath;
     public string SaveToPath;
 
     public void GenerateSilhouettes()
     {
         SilhouettesToCreate = new List<GameObject>();
         var entries = Directory.GetFiles(LoadFromPath);
 
         foreach(var entry in entries)
         {
             if (entry.EndsWith(".prefab"))
             {
                 Debug.Log(entry);
                 SilhouettesToCreate.Add(PrefabUtility.LoadPrefabContents(entry));
             }
         }
 
         foreach(GameObject go in SilhouettesToCreate)
         {
             var sc = go.GetComponent<StructureComponent>();
 
             var silhouette = Instantiate(go);
             DestroyImmediate(silhouette.GetComponent<StructureComponent>());
 
             var scs = silhouette.AddComponent<StructureComponentSilhouette>();
 
             scs.componentType = sc.componentType;
             silhouette.name = sc.name + "_S";
             silhouette.name = silhouette.name.Substring(silhouette.name.LastIndexOf(@"\"), silhouette.name.Length - silhouette.name.LastIndexOf(@"\"));
 
             Debug.Log(silhouette.name);
 
             scs.pivots = new List<Transform>();
             foreach(Transform t in silhouette.GetComponentsInChildren<Transform>())
             {
                 scs.pivots.Add(t);
             }
 
             scs.comp = go;
 
        
             PrefabUtility.SaveAsPrefabAsset(silhouette, SaveToPath + @"\" + silhouette.name + ".prefab", out var success);
             if (success)
             {
                 Debug.Log($"Successfully created prefab at {SaveToPath + @"\" + silhouette.name + ".prefab"}");
             }
             else
             {
                 Debug.Log($"Failed to create prefab");
 
             }
 
             DestroyImmediate(silhouette);
         }
     }
 }

the problem here seems to be the scs.comp = go; but i cannot figure out why that is not working. Any help would be appreciated.