Board Thread:Questions and Answers/@comment-5602817-20140604122856/@comment-34326521-20140607181010

Assuming Azmuth made the Omnitrix properly, it wouldn't glitch. However, assuming he didn't plan for every contingency, but still wanted it to be safe, I'm assuming it first converts Ben into energy, which it stores inside itself, and then changes his DNA, before reassembling him in his new form. If it glitched during the first or last parts, Ben would most likely die. If it glitched between those processes, Ben would simply be stuck in the Omnitrix as an energy signature.