When swapping boards, ensure that the Apple and the servo controller are both off. Handle the boards carefully to avoid static damage (earth yourself by holding onto an earthed conductor, hold the boards by their edges). Take care to note the orientation of the various cables that plug into the boards, and write a note on the board that you removed so that it can be fixed.
If the telescope isn't driving correctly (e.g., if the RA motor rotates too quickly, incremental encoder counts will be lost), you could try to adjust the potentiometers on the front of the RA and/or Dec board. The output voltages can be sampled between the two pins just below the potentiometers: the correct values during a slew are about 0.5V and are written on the front panel of the servo control box.