After i run “mailbfr -f” to fix my cyrus database, all mail shows up as unread.

Unfortunately we haven’t found a safe way around this issue yet. You’ll have to live with it. Important: "mailbfr -f" should only be used if your database is corrupted, not just for the sake of it and not just to recover a single user. If you need to fix a single user, issue "mailbfr -m username".