We have moved emails in a postfix server from huge mbox files to MailDir, but when trying out one Outlook client, found that it redownloads all mail as duplicate unread messages.
This is not really a postfix problem. Instead the issue probably is the way you converted your email from mbox to maildir. If you do not preserve the message UIDs when converting from mbox to maildir, the client can't tell that the messages are the same, and will therefore re-download them.
It would be helpful to know which IMAP/POP software you are using.
You might find the information on this dovecot page useful even if you are not using Dovecot as your imap server.