Well, you may be luckier than I had originally anticipated. After some research and digging around I've found this:
http://www.firstpr.com.au/web-mail/mb2md/http://www.qmail.org/mbox2maildirUsers maildir's are stored in /home/e-smith/files/{username}/Maildir/
The converse to what you want to do is already a qmail command called "maildir2mbox", so I assumed a mbox2maildir would exist. You appear to be a power-user so I'm sure you can figure this out, good luck. Please backup those mbox files before you run this in the event it hoses. I'd try the one providied by qmail.org first, then default to the one on .au
Let me know if this works, take good notes along the way, and this would be something that would be useful in a FAQ.
Hope this helped, please let me know the outcome,
Nathan