Unfortunatly there is not much we can do about that.
You cannot remove things from prefabs when they are sapwned in a scene. So any script that tries to remove and replace something inside of a prefab instance won't work.
So the keep prefab link can only be used in certain things.
or could you add some part in the documents to explain the effect and known shortcomings of `Keep Prefab Link` option.
It's ok for me personally, but I think it's better to add explanation somewhere.