Hi Ryan, Sorry for the delay.
We actually found a work around to the issue, and these were my steps in case it helps anyone else:
On partners computer add empty Game Objects to the prefabs and save them.
On my computer, make some changes to the prefabs that were causing her problems.
Check in my changes through the check in window
On partners computer pull the changes, and it will ask to resolve conflicts due to those empty game objects
Resolve the conflicts by choosing the incoming changes
Unfortunately since the problem is now fixed, I can't confirm whether it was on Custom Components or not. I have since pushed additional changes to those prefabs that were initially not working properly and they somehow now work. If we notice this behavior again I will grab any related logs and take some videos of the issue occurring.