The way this sort of problem has been fixed in Texas since 2024 is to require that all ballots be sequentially numbered -- that is, they arrive at polling locations in packs of 50 or 100 ballots, each pack having sequentially numbered ballots, but the presiding judge takes 10-20 at a time, signs them, then shuffles them, places them with the serial number facing down towards the table, and voters get to pick one at random when they check in.