Clicking Stop seems to lose calibration.
The kind of makes sense because "Stop" is what you would click if there were an error condition where a head was "out of bounds".
Reaching for the power switch is probably a more sound idea because if the machine is out of bounds there is some chance that software has crashed or malfunctioned and the safest course of action is to push the emergency stop switch in.

Often the amount of calibration is a small amount but enough to throw off small parts pickup etc.
This can be remedied by "Reset to Origin" but "Stop" should really set a flag in software and trigger a Reset upon Starting up again.

This is something I have learned the painful hard way - and am about to add a sign on the machine for other workers.