A joint prefab which is applied as an override to another prefab loses all data when its prefab is deleted from the project. Refer the attached video.

Steps to reproduce:
1) Create a new project
2) Create an empty gameObject > Create a prefab out of it. Call it prefab 'A'.
3) Create an empty gameObject > Add component Character Joint > Create a prefab of this gameObject. Call this prefab 'B'.
4) Add B as a child of A > Apply override.
5) Duplicate prefab B
6) Delete prefab B from the project

Actual result: Prefab B which was overridden loses all data in hierarchy and creates an empty child gameObject as well.
Expected result: Prefab loses instance in hierarchy as it's been deleted from the project.

Occurs on: 2019.3.0a4, 2019.3.0a1
Not reproducible on: 2019.2.0b4

Environment: Both Windows and Mac