How do I Apply a prefab without the coordinates of its children resetting to (0,0)?

When I'm working on some of my prefabs and would like to Apply my changes an issue keeps coming up where it resets some of the prefab's child elements to (0,0) coordinates. Has anybody found a work around for this?! It's really ruining my ability to work on my complex UI Prefabs because anytime I try to save a change, it just resets children to (0,0).

Related Documentation:

1. Issue 968969
2. Issue 964111
3. Issue 966172
   

 

Conversation is going on here and here. So solution so far. Very frustrating