I am not 100% because I do not use outlook anymore but doesnt it have a backup feature? Why not tell it to archive all emails older than 12 months and burn that to a cd for archival purposes. That's if you want to save all of that mail.
This solution is kinda off the wall but hey:
Sign up for a Gmail account. Add the pop account. Tell it to pull all messages. Then you have it all saved and easily searchable. Then you can wipe all the mail off the server and start from the beginning.
It seems that he may be deleting the mail in outlook however the since it is storing a copy on the server it is always there (on the server).
Switching to IMAP would help. If he deleted mail in outlook, (thunderbird.. switch. ) it would also be deleted on the server.
This is absolutely it.
One of the suggestions about getting a gmail account is pretty cool, but is it possible to make a backup that I could save on the server in a rar or tar format in case a restore is ever needed? And how would I delete the entire mail file/folder on the server?