You'd have to keep a list within your client, I think. I did a POP3 downloader that can download a particular message using its index number, but I'm not sure if they get renumbered when an email is deleted. The only other option I'm aware of would be to scan the headers like you say... POP3 servers are pretty dumb.
I guess you could store each read email's index and messageid in a list and check against it when trying to download email number 'x', only checking all the headers for the messageid if it doesn't match -- this may help to answer the question of whether they're renumbered when one is deleted.
I guess you could store each read email's index and messageid in a list and check against it when trying to download email number 'x', only checking all the headers for the messageid if it doesn't match -- this may help to answer the question of whether they're renumbered when one is deleted.