Just guessing, but I hate to see a machine down.
Sounds like a loose/intermittent connection/wire, and I'd put in a call to Tech as someone is usually on call.
But, before that, Power down Everything, and pull the plugs/breaker and let it sit for 10-15 minutes.
Power up and try a UR....then maybe read UT and do a Packet ET test for comms.

Maybe watch Andrew's vid on replacing control board, and see if you did anything differently?
https://www.youtube.com/watch?v=3iwKFDER494
It may not be exact, but should be similar.

I get that grinding noise in X if I'm rushing things as computer first boots up, and I do a C3 while the computer is doing startup things, but that goes away in a minute.

Going to be a pain isolating it though.
Hope you get sorted soon.
scott

Oh, On our 2 Desktops, we never once had the clip on the spindle/collet/bit....we put it on one of the the leveling legs, and it's lived there ever since.
Test and see if you can do the same?
So long as when you touch the Z plate to the bit EVERY time you Z-Zero, and get a green light on Input one...you're good to go.