Correct me if I'm wrong here big cat, but if memory serves, the compressor shouldn't kick in at all without the system being pressurized, should it? The compressor idler pulley should just spin freely without the clutch engaged....as long as theirs oil within the system to keep it lubricated, I don't see there being an issue....at least for short term use?
But I agree.....getting it all done at once would certainly be the best option.