hmmm... if it was a lot hotter then this suggests it was being overdriven (wrong current limit) or was in a state of stall (mechanical binding) All the motors are permanently energised so should all get to roughly the same equilibrium temperature. At high temperatures the motor could lose power (magnetics lose force with temp) and therefore a 'down' step could miss-step so the returning 'up' step is too far up... hence the decreasing z-depth over time...

The cutter you were using was a plunge type? you weren't trying to plunge something with no cutting tip? that would stall the motor or at least make it work hard...