PrefabUtility.ReplacePrefab trouble

Hi, there! PrefabUtility.ReplacePrefab is very useful to make prefabs from gameobjects. With colliders, materials etc. However, when I change one of the gameobject's shader variables, it won't save gameobject material at all. So I get a prefab without a material.

Any ideas how to silve this?

Thanks!

//Problem solved. U just need to save materials as well, cause unity use instances of materials if u don't use sharedmaterial.