A prefab with an old library representation will display different states in Prefab Edit Mode and in its instances in the Scene

To reproduce:
1) Open the attached project
2) Create an empty object and create three empty child objects on it
3) Add the script in the project to the parent object
4) Make the parent object a prefab
5) Go to a file viewer app (Win Explorer/Finder/Files), and open the .meta file of the prefab in a text editor and note down the guid there
6) Find the same prefab in Library folder through the guid and copy it in a separate location
7) Go back to Editor
8) In the parent object, attach the child objects to the script component in the inspector
9) Save and close the editor
10) Take the files you saved in step 6, and paste them back into the library, causing it to retain the old reference
11) Reopen Unity
12) Check the parent object in scene both in and out of Edit mode

Expected: It should show an identical setup
Actual: The non-edit mode object has no references attached in the inspector. In edit mode, they are still correctly shown.

Reproduced in 2018.3.0b1, 2018.4.11f1, 2019.2.9f1
Not reproduced in 2019.3.0a1, 2020.1.0a8