To reproduce:

1. Open the project, attached by tester
2. Select tree_sml_2 object in the hierarchy
3. Move said object in the scene view
4. Undo the changes
5. Observe the object in the hierarchy

Expected: undoing changes in the prefab with missing script references should not break the prefab
Actual: undoing changes in the prefab with missing script references breaks the prefab

Reproduced in 5.5.2p4 5.5.3f1, 5.6.0f3, 5.6.0p1, 2017.1.0b1