You're probably trying to use 2 accounts on the same server. Try
renaming the old account first.
Anyway, for pop3 the export/delete/create/import route is probably the
best way. For imap, it is much easier: for each account, go to
about:config and change @
mozilla.org/msgstore/berkeleystore;1 to
@
mozilla.org/msgstore/maildirstore;1
Restart Thunderbird immediately and all messages will be downloaded again.
You can delete the old "folder" files from your profile afterwards.