You could keep the ballot sealed but tied to the voter's ID. Once the polling center closes for every mailed-in ballot they check if they have an in-person vote. If so, they discard it, otherwise they add it in the urn before it's opened for counting.

This is actually how it works in Sweden. They check the voter list whether the person already voted during the day and discards the mail-in if so.

> Once the polling center closes for every mailed-in ballot they check if they have an in-person vote

Agree on keeping votes sealed until live polling closes. But there is no need to check every mailed-in ballot against in-person votes.

Instead, when a mailed-in ballot arrives one marks the voter rolls. When a voter checks into a polling place, the rolls are anyway consulted. At that time, if a live voter shows as having already voted: that ballot is found and destroyed, and the voter given a fresh ballot to cast.