There is a way, but it is complicated and risky. You might end up with inoperational mailboxes. Do this at your own risk. I assume no liability for any data damage that can result from interfering with the email storage algorithms manually.
1) Check /var/qmail/mailnames/<domain>/<email name>/Maildir/cur and /new what timestamp the individual mail content files have. If all "old" duplicates have a timestamp "older than n days" compared to the new, you can use a command like
# find ./* -mtime +n -exec rm {} \;
to remove all the files older than n days, so that only the "new" imported files are left. So you can get rid of the duplicates.
If the files cannot be grouped by age, e.g. if your import has restored the original file timestamps, you cannot get rid of the duplicates.
In any case, (1) will destroy the index of the mailbox.
2) So if you should succeed in (1), you need to rebuild the index of the mailbox. This could work:
# doveadm -D force-resync -u <mailboxname (email address)> '*'
Proceed only if this does not display errors.
# doveadm fts rescan -u <mailboxname (email address)>
# doveadm index -u <mailboxname (email address)> '*'
Again, no liability for any damages this might cause. I think it's a risky thing to do.