it is best if you keep the chains 'in step' with one another, which means rotating them fairly often, depending on how fast you wear chains and how many chains there are in rotation (three or four isn't uncommon).
If they get out of step then you can end up with a virtually unworn chain trying to work on more worn sprockets; this can make for skipping. It is unlikely that you will end up with a worn chain on newer sprockets this way (except in virtually unused gears) but if you do it will usually run OK A bit noisy perhaps) but the wear rate will be much higher than normal.
cheers