When you open a prefab for editing, you are actually editing the “prefab asset” itself. When you edit a prefab asset (or any asset for that matter), it can not hold scene object references as usual anyway (that is a Unity thing). So even if you were able to edit the prefab asset directly without opening it up in the prefab editor, you would still not be able to reference scene objects like Paths are.
What you want to do instead, is simply edit the “prefab instance” that is in the scene directly, without opening it up in the prefab editor. This will of course “override” the master prefab asset, but this is generally speaking how Unity works 🙂
Once again, assets (like prefab assets) can not have scene object references anyway. You can of course if you want, make the Paths part of the prefab if that fits your workflow.