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How to remove messages from server when using POP/IMAP combo?

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I have an email account with our ISP that is shared by two users.

One user is IMAP. (My boss.)

The other user is POP3. (Me.) I use Thunderbird 52.8.0 and settings for the account are: Leave messages on server -> For at most 14 days

"Until I delete them" is NOT currently checked.

Despite my Thunderbird settings, messages are not being removed from the server. I suspect that IMAP and POP3 being used at the same time may be screwing something up. We have other POP3-only accounts with the same ISP and they work correctly.

The account is now receiving quota warnings and I'm not sure what to do. Thanks!