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I do not have hydraulic brakes, so if yours are, you should ask someone that knows more than me how to prep a bike for transport if there is no rotor inside the disc brake unit. You do not want your pads to be too close together to get a rotor back into the unit when you reassemble the bike.
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You'll want to insert 1.) a guard or place holder that stands in for the rotor contact point between the brake pads, preventing the caliper pistons from coming out and 2.) a guard on the brake levers that prevents them from being actuated.