Ordinarily, I hate to blame the user, but there are two things going on here:
1) The user needs to learn how to use folders for organizing mail. Leaving everything in INBOX is not the way to go.
2) POP3 + leave mail on server + 30k messages = Somebody loses eventually.
POP3 is designed as a protocol that allows for local mail storage. Your mail reader connects to the server, authenticates, downloads the messages, deletes them, and then disconnects. If the "deletes them" step doesn't happen at least regularly, you run into problems like this.
IMAP4 is a much better protocol for most people today. It allows you to have access to exactly the same mail with exactly the same folder hierarchy from any computer in the world.
If your user's mail server allows him to store 30,000 messages on the server but doesn't support IMAP, that's just miserable. I know "find a different provider" isn't an option, but perhaps asking for IMAP support (if it is not presently available) is. If IMAP can't be had, then definitely pay attention to items 1 and 2.