How do I get rid of duplicate "in" and "sent" mail boxes?

I have installed a new version of Thunderbird on a new machine and used Easy Transfer to move my mail boxes etc from my old machine. The problem is that I now have duplicate "in" and "sent" mail boxes. New in and sent mail only appears in one of them but I can't delete the other. I have deleted all messages in the extra "in" box (they were all duplicates) but have not been able to do the same with the messages in the duplicate "sent" box because the "deleted" folder where they would go is not big enough to take the 16000 messages in there (when I "select all" and "delete" it just says "deleted folder is full" when in fact there's nothing in it; I am assuming this just means it would not take all the messages to be deleted). Help please!

Try rebuilding the global data base
https://support.mozilla.org/en-US/kb/rebuilding-global-database

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