I don't know of course what Walmis did with your motor, but in general the auto calibration in the VP config is supposed to be a user level exercise that can (and must) be performed whenever you change something, like installing a throw limiter, change or re-tighten the belts etc.
So I think it is save to say, that you certainly won't break anything if you do a calibration. Just look at the monitor in the config tab and see if everything is properly centered. Otherwise do a calibration.