Repro: add a script to an instance with “public GameObject prefab;” then drop the instance’s prefab on that variable then apply changes, drop a few prefabs in the scene and click on “prefab” variable. What you’ll see is that self highlights instead of its prefab.
In 4.6 this used to work and keeping reference to the prefab asset.
In my little project, I used reference to prefab to get in-scene entities to register themselves to the pooling system and this no longer works. Is there a new way to get an instance’s prefab at runtime?