First of all, talk to the manufacturer of the unit.
Taking liquid into the compressor can be a real disaster for the most common type of compressor. It is likely that the manufacturer has specific steps for you to take, in order to reduce this risk.
Indeed, having the HVAC guy empty the system prior to transport is likely a good idea in any event. An added bonus is that you can do your hook-up before the refrigerant is returned to the system.