Steps to reproduce:
1. download and open "repro.zip"
2. open "new" scene
3. delete "script" in assets folder
4. press apply on "cobe" in hierarchy
5. prefab breaks

Expected results:
Prefab shouldn't never break
Actual results:
Prefab instance breaks when applying it with delete script attached

Workaround:
Remove deleted script from prefab's instance and press apply. This will restore connection between prefab and it's instance.

Reproduced on:
5.3.6f1
5.4.2f2
5.5.0b1
5.5.0b11