Bartman
Welcome to MultiRotorForums.com!!
No, do not remove the board to calibrate the mag. You want to calibrate it on your bird with all accessories (gimbal, camera, etc). You want to calibrate the mag with your birds inhearent magnetic fields present.
The reason the accel needs to be redone is most likely the recent change in how AH and AL use all sensors now.
when compasses are being calibrated in full scale aircraft the engine is running, all accessories are powered, and the various lights/strobes are on. to really do this with a multi-rotor heli then it's beginning to look like we should have motors running while doing the procedure.
anyone?