To reproduce:

1. Open the project, attached by tester
2. Open scene if not open
3. Add 400 GameObject prefabs to the hierarchy
4. Select the first prefab in the hierarchy
5. Unfold prefab
6. Unfold GameObjects "1", "2", "3" and "4"
7. Select "4" GameObject
8. Move it in the scene
9. Undo the changes

Expected: undo should not be slow when undoing changes to a complex prefab while there are lots of instances of the prefab in the scene
Actual: undo is slow when undoing changes to a complex prefab while there are a lot of instances of the prefab in the scene

Reproduced in 5.6.0f1, 5.6.0f2, 5.6.0f3, 5.6.0p1, 2017.1.0b1
Did not reproduce in 5.5.2p4, 5.5.3f1
Regression introduced in 5.6.0f1