What stops any stones getting stuck is the colonic/colema within 3 days after the flush, not the malic acid. Using malic acid/apple juice just means that the flush isn't difficult, as larger stones are more difficult and painful to pass. Still, many have passed large stones with no pain, but the colonic is important.
Hope that helps! By the way, many have done the flushes without colonics (and used enemas or some other colon cleasning products) and not had stuck stones. It's rare to happen. If you are in very poor health, I suggest you follow his protocol tightly as you may have many large stones.