Having the same issues with missing inbox with IMAP account, i can successfully enter INBOX as root folder path and when prompted to "refresh" folder list it updates successfully. Yet if i right-click my account and select "download all folders" the inbox then disappears

also if a do not "download all folders" emails seems to sync but i get pop up errors

Could not download new messages from IMAP server

Error in IMAP command received by server.

Configuration:
   Account: Spin.net ***********
   Server: pop3.spin.net.au
   User name: *********
   Protocol: IMAP
   Port: 143
   Secure(SSL): 0
   Code: 80004005

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