Your election process may vary, but usually mail in ballots are in a certification envelope with your name, address, and often a declaration of eligibility, voter signature and witness. Digital methods may have a barcode encoding this information, easily readable only by an election official.

That identification can be used to trace your ballot if damaged/lost and to check for eligibility and that you only voted once.

The contents are then removed from the certification envelope and the secrecy envelope containing the ballot is added with other votes and anonymised.