POP3 provides a special (temporary?) id that stays unique and unchanged at least during the time of the session, even when you delete messages: the uidl. You can use that as the basis for a better tracking system for which messages you've read: with two uidl hashes, you have both the old and the new message number, and by inverting one hash

%msgnum = reverse %uidl;
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you can map

old message number -> uidl -> new message number

or, in Perl:

$new_msgnum = $msgnum2{$uidl1{$msgnum}};
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As I currently don't have a pop3 mailbox available for testing purposes, I can't really test it and the code is just pseudocode, just giving a general outline, and not real working code.

But what I don't get... as long as the connection isn't closed, the messages aren't renumbered, or are they? That's how I remember it.