Thanks Robin. Your advice is too late for the 1000+ messages I lost by deleting my old account settings, but it could prove useful in the future. As it is, I've simply set up rules to filter messages from different places (like my pop-accessible webmail account) into separate mailboxes.

Just to clarify my earlier post-- deleting an account in the Preferences-Accounts dialog seems to delete all of the messages for that account that are sitting in the Inbox. But it doesn't seem to affect messages that were filtered into other mailboxes (like a mailing list mailbox I had set up previously).