GaryYes, if you go to the Foot Switch 1 page for your organ layer and set both On Control and Off Control to OFF. This will disable the footswitch for this layer.
If you want to control the Leslie with another controller, e.g. another footswitch or SW1, go the the appropriate page for the controller, set On Control and Off Control to 64 (the controller number for the sustain pedal) and the On and Off values to 127 and 0 respectively.
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