Any card that isn't specifically mucked by another player could be audited... I think. So that would be: the players own cards, the burn card, the flop, turn, and rivier cards (maybe), any card that makes it to a showdown, plus any remaining undealt cards in the deck. That's quite a few cards that could be audited. The audit wouldn't be airtight, but I see it as a step in the right direction.
Something else to think about: In a head's up situation, a comprehensive audit of all un-mucked cards would allow a sharp player to figure out the hole cards of their opponent (from the previous round) by process of elimination. Maybe that's OK if both players are privy to the same information, but it certainly changes the character of the game.