I now remember what I did to create these duplicates.
Back when I first switched from Windows to Mac, I thought it would speed up the Mail App startup and search functions if I archived old mail out of the app. In my Windows days, I would stop the app, rename the mail file, then restart the app. Id keep the old/archive files for future reference, but as long as they were out of the main mail file, Outlook ran faster.
Not knowing that this duplicate pointer thing was happening, it appears that I did this file renaming nine times at three different points in time. It appears that each time I did this, MAIL would create another pointer so that it now thinks I have 9 of them - but in reality they all point to the very same single file.
Now that we know what caused it, any ideas how I can undo it?
The same 9 "On My Mac" folders appear in the mail navigation list, but there is only one real underlying folder. I know this because ~/Library/Mail/V2/Mailboxes only has one Archive.mbox. However, I noticed one look slightly different in the navigation list. I delete that one and the others disappeared...