Steps:
1. Make two prefabs 'A' and 'B'
2. Instantiate them both
3. Create a script and add it to 'B'
4. Delete the script asset
5. Add 'B' as a child to 'A'
6. Right-click on 'B' and choose 'Added GameObject'
7. Choose 'Apply to Prefab A'
==>
"You are trying to replace or create a Prefab from the instance 'B' that references a missing script. This is not allowed." - That is Ok
"ArgumentNullException: Value cannot be null. Parameter name: objectToUndo" -> Should not be here