Steps to reproduce:

1. Open attached project
2. Open scene "repro" and run it
3. Drag "Prefab" prefab to scene as a child of "GameObject"
4. Move created instance
5. Press ctrl+z and notice that prefab gets unparented and "GameObject" is disabled

Note: "GameObject" only gets disabled in Unity 5.6. On older releases object is still active - the unparenting, however, still happens. Also - this doesn't reproduce with "normal" prefab instances created using Instantiate.

Reproduced with: 5.4.0p2, 5.4.4p1, 5.5.1p1, 5.6.0b5
Not reproducible: 5.3.7p3