I used to be able to set my zero, carve for a few hours, and then completely shutdown the system overnight. This includes turning off the PLC. I could then start up the next day and the system knew where I had set zero the day before. I did this for at least the past year. Recently, I upgraded to build 644. It will return to the zero for the X and Y, but not the Z axis. I’m also hearing irregular stepper motor issues. Did something change in build 644 where it doesn’t remember the Z-axis zero? I’ve tried it a couple of times and have had to reset the Z-axis zero two days in a row. I’ve had an issue in the past with the ball screw mechanism and starting to think I may have an issue again.
The latest version of CM remembers X Y and Z but Z is not remembered until a bit goes to the BitSetter. You can have that happen in a couple of ways. One is to do a tool change. You can just leave the tool in the router but it will go to the BitSetter. The second way would be to load your file and CM will ask for the first tool and that will send the router to the BitSender. In the mean time you may get messages about setting zero but technically the Z is remembered. That change has caused some frustration among users but the Z is remembered the machine just does not know it knows it. 
I just rezero any time a powerdown is done, machine is so unreliable in every axis X being the least problematic sometimes off by 1-3 thou [not that it was marketed that way. I just know better at this point]. Even on a solid machine the switches plus the low polling rate of the SMC = do not trust for repeatability.
This worked perfectly. I’ve been doing epoxy inlays. Carve an area, pour the color, shutdown machine, let it dry overnight, then carve the next color. etc. I overpour a little high, so in the end, I can run a flat surfacing pass to even out everything back to “Zero” on the Z-axis.
Carbide 3D should do a quick video tutorial on this. There are a lot of users that think that if they shutdown the machine at night, they will loose the zeros.
Thanks again for the great help.