After removing and re-adding an IMAP Connectivity synchronization, all emails that were already synced before gets duplicated. Maybe there is a way to compare the remote Message-IDs with the local IDs at the first sync?

This behavior bubbled up after changing the 'IMAP Retrieval Interval' (IMAP Protocol settings) to a lower value (2 minutes) but still had to wait almost 10 minutes (the default value) before the new mail was synced. it seems that the interval change is only applied after restarting the SmarterMail Service? Because after a restart, the mail is correctly synced according to the new interval. I have not tested the interval change for the POP Connectivity synchronization.

Another improvement could be to sync the mailbox state back to the synced IMAP account. I think this is a lot of work to implement, but it makes it very easy to keep the remote Inbox (and possibly other folders) clean: moving/deleting an remotely synced message would also move/delete it in the IMAP account.