Steps to reproduce:
1. Open the attached project
2. Open "Block" prefab in Prefab Mode
3. Delete "Cube" prefab in Project Window
-notice that nested Cube prefab GameObjects now appear red in Hierarchy due to missing reference
4. Open "Block Variant" prefab in Prefab Mode
-notice that cubes are still there for the "Block Variant" prefab and do not appear red in Hierarchy
5. Open "Block" prefab in Prefab Mode again
-notice that Cubes are now gone and replaced with "Missing Prefab"
6. Open "Block Variant" prefab in Prefab Mode again
-Cubes are still there, Base Prefab and Variant Prefab are no longer in sync and the Prefab Variant has no overrides

Expected result:
Base and Nested Prefabs remain in sync
Actual result:
Cubes are still present in the Prefab Variant but not in Base Prefab

Reproduced with: Version 2018.3.0a2 (e9113db2e9bf)
Thu, 14 Jun 2018 21:56:37 GMT
Branch: prefabs/improved