I've done this many times and I've never had any side effects, so your Pokemon, originals and cloned, will be safe. I would recommend that once you're finished cloning them to save your game and take out the AR. Try your best not to play while it's in your DS cartridge slot. It's never happened to me personally but I've heard of problems occurring when the AR is left in for too long while not being used. Otherwise you should have no concerns.