popstat() returns the number of undeleted elements. That should be related to the highest numbered message if you haven't deleted anything this session.

uidl( msgnum ) returns the UIDL of the given message.

Since POP3 servers tend to number messages from oldest to newest, if your last message's UIDL has been seen, all previous ones should have been seen. If it hasn't, you could decrement the message number and get the UIDL of each in turn until one you've seen. Once you've seen one, you've seen all the previous ones.

As a side note, you may want to consider downloading and storing the messages themselves in the database, if that would work for your application. Unlike IMAP, POP3 is not really designed nor intended to be used as long-term storage of email messages. VPS servers tend to have a huge amount of disk space and just a bit of memory. Using the database for your storage allows you to query the DB and grab just the information you need into memory (apart from overheard of course).