I started a print last night and then left it for about an hour. When I returned the print looked really odd and then I noticed the left side Z-axis stepper motor didn’t appear to have moved nearly as far up as the right. Probably a difference of an inch or more. I stopped the print and let everything cool, but now I don’t know how to get those motors back in sync or lined up with each other. Suggestions?
With the machine off, you can simply turn the threaded rod couplers by hand. Measure from the bed to the X-axis rod, and try to get as close to parallel as possible. Any remaining small difference will be handled by the bed probing/compensation.
It is probably best to disconnect (unplug) the motors before turning them by hand. I never do, and have never had an issue. But it is theoretically possible for the current created when manually turning the motors to damage the electronics.
I would be very concerned about the cause. You could have an intermittent connection to one motor, or a bad wire, a failing motor, or a loose coupler. Check all the connections carefully, and make sure the set screws in the couplers are all all tight. Watch the next print VERY carefully, and be ready to hit the power switch if you see uneven travel.