As long as windows is present on the drive it will have no problem swapping the drives around. But make sure that the drives are compatible with the other motherboard if there IDE or SATA. When connected ensure that the master is the first one on the IDE cable and the jumpers are set correctly.
Running the previous master as a slave will probably be easier, just move the jumper across.
Running the previous master as a slave will probably be easier, just move the jumper across.