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You don't say what mail client you're using, but in Apple Mail, you can just select all and drag them to a new mailbox or folder. It will take a while, but it doesn't really require anything from you.
Chuck ___ "Instead of either 'multi-talented' or 'multitalented' use 'bisexual'."
There is also a very useful command line script called imapsync that can be used for creating complete functional mirrors of email accounts - i.e. everything in the right folders with the right flags set. If you have rsync/SSH access you can mirror your website files as well. Be sure to do a database dump if you have any database content.
I've never actually used it, but what does the Archive Mailbox function (one of the options in the Mailbox menu) in Mail do and would it be what qnc needs?