Steps to reproduce:
1. Create new project
2. Create new scene
3. Drag the main camera (or any other game object to Project View to create a prefab)
4. Save the scene
5. Delete the prefab
-> the main cam object name becomes red and all component settings are still there (correct)
6. Double click the scene to re-open it
-> the main cam object becomes red name "Missing Prefab", and all component settings are gone (wrong)

Expected: After reloading the scene, the GameObject is still there as per step 5.
Actual: The GameObject is entirely missing, only left is a reference to it as "Missing prefab" in Hierarchy

Reproduced on : 5.4.5p1, 5.5.3.p3, 5.6.1p1, 2017.1.0b5, 2017.1.0b6