Steps:
1. Create a new project
2. Add GameObject and assign any script to it
3. Convert to prefab
4. Delete script from Project Browser
==> Now we have Prefab instance with missing script
5. Select Prefab instance and remove missing script component
6. Look at Override window
==> It has "Unused override"
7. Remove unused override
==> Missing script is back to the instance

Please, take a look into attached movie for details