My D800 Crashed - Nikon Service in Los Angeles is Stumped.

You got second best case scenario (the first best case is when camera is working fine ) your camera has a reproducible issue and easy to troubleshoot if Nikon has spare boards; if they don't have spare boards you may get a new camera.

The only worries I would have are related to mechanical alignment of parts involved in the optical process; it is possible that they won't need to remove those parts to fix the electronic issue. I would thou roughly test the focus and look for issues like soft corners after repair (just in case). I would not be worried about the electronic issue, that is easily fixable.