Reproduced in 4.2.a3.

1 Create new project and import character controller
2 Put 2 instances of 3rd Person Controller.prefab to the scene.
3 Choose 1 and rotate it-

You will notice 2 things:

1)Rotation field in Transform inspector doesn't become bold
2)If you apply modifications to the prefab they are actually applied but the instance of the prefab already present in the scene (second 3rd Person Controller) is not updated