Save Waypoints to PreFab

I’m hoping someone here can help me.

I have dragged a PreFab into my game, edited it (waypoints) and want to save it now.

However, this does not work. It’s my first try in Unity and so far it worked fine.
Can someone tell me why this is not possible?
I can’t edit (drag in) these waypoints directly in the PreFab either.

Prefabs cannot refer to objects inside a particular scene. How would that work when you copy the prefab to a new scene?