Steps:
1. Add two GameObjects to hierarchy "P1" and "P2"
2. Convert them to prefabs
3. Make P2 child of P1
4. Save the scene
5. Drag P2 to Project Browser and choose "Prefab Variant"
6. Select P1 and Apply All in Overrides window
7. Double click on scene asset (to reload it), choose "Do not save"
8. Drag extra P2 GameObject to the last child of P1 (if it is not there yet)
9. Select P1 and Apply All in Overrides window
==>
Prefab is reimported and became broken.
Prefab instance has missing asset type

Please take a look into movie for details
Regression from 2021.1.0a2