How do I write a Mail.app rule to mark messages as read in one mailbox but leave them as unread in my in-box?
It seems Mail 6.0 in Mountain Lion has fixed this for me. When I have new mail it shows as unread in both my in-box and my archive mailbox. And now, when I read it in my in-box it gets marked as read in both my in-box and my archive mailbox. Chalk one up for Mountain Lion.