I wouldn't have thought so...
Aslong as you lower vehicle to the bump stops then remove battery connection, jack up the vehicle on the axle as per normal, place axle stands under the chassis, then lower the vehicle onto the stands, remove wheels....
Then disconnect the pneumatic pipe from both air bladders (beware - a small discharge of air may happen), then lower the axle as far as it will go and remove the air bladder, replace with the new air bladder, Jack up the axle to collapse the air bladder and refit the pneumatic pipe and road wheels, continue to jack up the vehicle and remove the axle stands, lower vehicle to ground.....repeat with rear axle.....Replace Battery connection
This way, all the system knows is it was lowered to the bumps and nothing more and because it is starting from the bumps it should be OK, if you now run the vehicle and then select standard ride height, it should raise.
Just My Opinion, the Wammer and Datatec know this system better than most, so maybe they can ellaborate and expand.