Have you considered using IMAP on the phone? When you download and delete messages with your primary PC, the messages would automatically disappear from K-9 Mail during the next sync (with IMAP).
Long-term there’s a decent chance POP3 support will be removed from K-9 Mail. We don’t support the download and delete from server model that POP was built for. Also, we don’t want to be the single store of a user’s messages. That will only end in tears if there’s a bug in K-9 Mail that destroys the database, if the device is lost or stolen, or if the device breaks. For non-rooted users it’s not possible to get to the database if e.g. the app doesn’t start anymore due to another bug.
I’m not saying POP3 is not useful. But I think a mobile app with proper POP3 support should offer extensive backup functionality and the capability to manage local messages and folders. K-9 Mail is not that app and likely won’t be in the future.