[New-Editor] When reloading the editor scripts and you have a prefab open, it breaks prefab mode

[PaperPrototype]

Describe the bug
When reloading the editor scripts and you have a prefab open, it breaks prefab mode

To Reproduce

1. Open a prefab and start editing it.
2. Create a new script and reload the editor.
3. The editor will reload and load the prefab scene. You'll notice all the special prefab stuff is gonzo

Expected behavior
Prefab mode should not break and should be preserved across editor restarts