Hey DocShay,
my (rather long) experience with Raspberry Pis is that they are not as robust as one may think. I had the HDMI output suddenly fail, while the rest worked perfectly (running programs, remote operation, remote login, etc.). I reinstalled all Raspberry Pi firmware packages, but no success. I had to replace the Raspberry Pi 3B to have a working HDMI output again. (after I ordered a Raspberry Pi 3B, it was out of stock – seems to have been the last one 
)
Be sure that your CNC machine is correctly grounded and bonded.
Should you open the controller (or any computer), e.g. to remove the internal SD card, I suggest to always work ESD-safe , i.e. that you put it on a grounded antistatic mat (as shown on image) and that you wear an antistatic wrist strap.
