When you remove the account, Thunderbird has no more visibility of any messages which may still be on your disk and previously did belong to the IMAP account. Removing the account in Thunderbird does nothing to the messages on the server. You can also safely delete any messages which which may still be on your disk and previously did belong to the IMAP account. I'd suggest to create a full profile backup prior to remving the account though. https://support.mozilla.org/kb/profiles-where-thunderbird-stores-user-data#w_backing-up-a-profile