Not sure that speed and acceleration make much difference to heating with stepper motors. Might be worth seeing if your drivers have a "half current" option for when the motor is stationary, though, as this can help reduce heating. I don't think that heat effects in the motor would cause it to suddenly stop and start either. Might be driver overheating and faulting, though? Does your machine monitor fault output from the drivers? What drivers/motors/supply voltage are you using? Any obvious signs of binding/mechanical stickiness (motor trying to move but just making noises)?

Last time I saw this effect was on my 3D printer and in that case it was excessive motor current causing the drivers to overheat and go into shutdown until they cooled and started up again - having lost sync.