That should be fine, although I'd actually rather track down the source of the problem
How did you assess that the calibration had completed? The most reliable way to see if it completed is that after you think you have completed the calibration you could try to arm the aircraft. Provided you have the arming checks enabled you would get a message telling you a reboot is required after the compass calibration has completed. The other way is by listening to the buzzer tones to assess if it has completed, but that of course is only possible if you have a buzzer connected.