It depends on the magnet material's coercivity and the field strength. If the rotor is removed, the magnetisation of the poles may shift from normal to the pole surface to transverse, towards the adjacent pole, following the lines of flux, significantly reducing the effective field strength when it is reassembled. Whether or not this will happen depends on how the rotor was magnetised and assembled. Higher power, lower mass motors are more likely to be affected. The issue can be avoided by sliding the rotor into a closely fitting tubular magnetically soft shunt, thick enough to carry all the flux as it is removed. For PM motors with magnetised stators the shunt is slid in in place of the rotor.
As long as you can leave the rotor in situ and don't disturb the magnetic circuit, increasing the rotor gap, you wont have any problems. For high performance motors, you may need to rigidly clamp the shaft and body so that the rotor doesn't go off-center increasing the gap at one or ,more poles when you remove an end plate supporting a bearing. Once you have access, you can shim the rotor with not-magnetic material so you can un-clamp the motor to work on it then reverse the process to reassemble.