The absentee ballots are kept in individual sealed envelopes until after the polls close. At that time the election judges compare the absentee ballots to the voter sign-in book, and any absentee ballots submitted by people who later showed up to vote in person are discarded. *Then* the remaining envelopes are opened and the absentee ballots are counted.
My wife is an election judge, and we're looking forward to a long and pretty miserable night next Tuesday.
Man, I bet this will be a miserable one. My prayers go out for you both.