Emptying a Mailbox via Command Line

Hi all, I'd like to regularly clear out my spamassassin junk imap mailbox about once a week or so to keep things tidy after sa-learn has done its thing with them. I thought I could do it just by running a command to delete all the .123 type files in the box, but they still appear in webmail, though just as empty messages. I figured this was because of the cyrus.* files in the mailbox, but removing those leaves the account undeliverable. Any ideas? Thanks! :)