Count duplicated messages for mailbox:

doveadm -f table fetch -u user@mailbox.org \
  hdr.message-id mailbox INBOX | sort |uniq -c | sort -k2nr | \
  awk '{printf("%s\t%s\n",$2,$1)}END{print}'

De-duplicate based on the message-id (arg -m):

doveadm deduplicate -u user@mailbox.org -m mailbox INBOX

Docs:

• https://doc.dovecot.org/main/core/man/doveadm-search.1.html
• https://doc.dovecot.org/main/core/man/doveadm-deduplicate.1.html