Can I delete duplicate messages under Maildir on the server?

After a client misconfiguration, many messages have been deleted. I restored them from backups, but now there are many duplicates.

I can identify them on the server, and delete them.

But do I need to also delete the dovecot.index files and/or other dovecot* files in the affected folders, or will these be automatically updated?

(My Dovecot version is 2.3.13, so I guess I should not use doveadm deduplicate which would risk deleting non-duplicate messages, according to the "doveadm-deduplicate deletes non-duplicates" thread here?)