I think I did something recently (it had to do with answering "no" when mutt asked me whether I wanted to purge deleted messages) that caused mutt to lose track of which messages had "D" (Deleted) flags on them.
Does anyone know what I did, and how to avoid doing it again? I think someone recently said on this mailing list that mutt does not have the ability of saving "D" (Deleted) flags. It seems odd that mutt doesn't support it, since there seems to exist ways to store these flags ("X-Status: D" in mbox, or put "T" flag in filename in Maildir/cur).