ReplacePrefab() resets transforms for instanced prefabs?

Hi, I have a problem with instanced objects getting their transforms reseted back to their initial Prefab transform values. All this happens when I re-import a model that is processed through a editor script in OnPostprocessModel(). In this script I apply BoxColliders, scripts and so on. Everything works great except for the transform-problem. Here's the code snippet I think is causing the problem.

//Instantiate the loaded model in the scene temporarily to make changes to var go:GameObject = GameObject.Instantiate(model, Vector3.zero, Quaternion.identity) as GameObject;

 //Search for prefab at path
 var prefabName:String = "Assets/Prefabs/LevelComponents/GroundComponents/" + model.name + ".prefab";
 var prefab:Object = AssetDatabase.LoadAssetAtPath(prefabName, Object) as Object;
 if(prefab == null)
 {
     Debug.Log("Couldn't find any prefab with the name: " + model.name);
     Debug.Log("Creating prefab: " + model.name);
     prefab = EditorUtility.CreateEmptyPrefab(prefabName);       
 }
 else
 {
     Debug.Log("Found prefab to update. Updating: " + model.name);
 }
 //Replace prefab with the modified GameObject
 EditorUtility.ReplacePrefab(go, prefab);

 //Remove the GameObject from scene
 Editor.DestroyImmediate(go, true);

So my question is if there's a way to update a prefab with "reimport" and process the model without reseting the transforms for the instanced objects in scenes? Thanks, /Rikard