So I updated to Unity 4.3.3 and since I have all my prefab links appear to have broken, they don’t appear broken but when updating a prefab it does not affect any of the prefabs in the scene.
The specific bug I’ve encountered relates to a building with lots of prefabs buried within the game object (props within a game level). Upon updating the game object is acting as the prefab and all the instanced objects (prefabs) within are now one with the master prefab.
It appears to be reproducible, updating the master prefab destroys the links of all of the prefabs within the game object, this was not the same in previous versions
There doesn’t appear to be any way to fix this and I’d suggest not updating to 4.3.3 if you have a lot of complex objects in your project.