It's going to vary county by county - but this is the purpose of provisional ballots. It's absolutely automated. The database knows if you've been sent a mail in ballot when you check in. If the system says you've been sent a ballot, you have to surrender that ballot to vote. If you don't have the ballot then you cast a provisional - which means it will not count if your mail in ballot has been received.
This is why provisional ballots are always the last thing to be counted. They have to verify that you no ballot case against your voter registration has already been cast. This isn't rocket science. Full proof? Of course not. Subject to human error? Of course. Is fraud possible? Like everything else in life, yes.
