I did a bit more playing around and the "filed" flag is a red herring. It's really any label that the imap server doesn't recognize that causes issue.
I was wondering why my deleted messages where getting cleared, then I realized what was happening: I'd read, reply, file, and delete my mail. Messages are marked "\deleted" and "filed" (or another imap label Exchange doesn't recognize such as "junk"). Since Exchange can't store the flag, the command fails so none of the flags are being stored. VM then syncs flags from the server, so my deleted flag is cleared from my inbox since the server rejected the store command. Attempting to store any flag the server doesn't recognize is causing none of the flags to be stored. I would guess the right thing for VM to do would be only attempt to store flags that are explicitly recognized by the server. -Kyle
