I assume that document ID should be the same for each duplicated doc, so if you delete one mail from Bob, the other one should dissapear also.
One thing that you can try is to move all mails from the inbox to a new folder. After that, you open the database with the Designer, go to Folders and delete the inbox, then do a Replace Design to re-create the Inbox.
Once everything is done, you can enter the mailfile and move (not copy/paste, just drag and drop) mails from the new folder back to the Inbox.
You may check then if the problem is still there.