Prefabs losing connection when placed in the scene.

We have been trying to upgrade our current project to the 2018.3 beta to test the nested prefabs and we are having an issue with the prefab loosing all the connections when placed in the scene. We can see in the prefab mode that everything is connected correctly, but when placed in scene it looses every reference.

The frustrating part is we have several people trying to update to this version, and some prefabs are ok for some and breaks for others, We have tried getting the project fresh from git, and deleting the library files, but now matter what we try, the disconnected prefabs are always disconnected.

 

Do you have any compile errors in the project?
If you had compile errors, have you tried reimporting the problematic Prefabs after fixing all compile errors?
Which beta are you using?

 

So we are using 2018.3 b5. I just saw your post, and I think that the reimporting of the prefabs will work, we are currently testing on a few different machines