[Dovecot] Converting mbox to Maildir, all prior read messages are downloaded as new

I am running dovecot 0.99. Everything works great; however, now I am looking at several different tools to convert mbox to Maildir. It seems the tools, mb2md.pl, perfect_maildir.pl, and others all do what they claim; however, when the messages are converted and they are stored in Maildir/cur, the email clients download these messages as new.

This typically wouldn't be a problem; however, I am dealing with 100s of users with 1000s of emails and this really isn't acceptable behavior to them. Any thoughts on how to correct this issue and prevent the client from downloading these messages again?

As a note, my test client is thunderbird and my preferred mbox to Maildir tool is mb2md-3.20.pl.

Thanks!