Project Steps:

1. Open scene "514GuerickesOrb12".
2. Game objects "SubjectToBug" parent is "OtherObject", change it to "Parent".
3. Save scene.
4. Load scene (Double click it).

Project Steps for new project:

1. Start a new scene and save it.
2. Create two parent game objects "First Parent" and "Second Parent".
3. Create a child game object "Child" under "First Parent", and then
create a prefab from "Child" by drag-and-drop.
4. Save the scene.
5. Delete the prefab in the project view, "Child" in the hierarchy
should turn red.
6. Move "Child" from "First Parent" to "Second Parent".
7. Save the scene.
8. Load the scene.
9. Notice that "Child" is still under "First Parent", regardless of your
change in step 6.

Reproduced: 5.0.1f1, 5.0.0f1