I’m not quite sure how this happened, maybe an iCloud thing but about 1 month ago I noticed 2 exact mailboxes for my main email address in Apple Mail. I deleted the mailbox, deleted the com.apple.mail.preferences, but it still appeared and repopulated itself from the iMap server. In Apple mail I only saw 1 account, but in the sidebar there were 2. Finally in the Mac “Internet Accounts” preferences pane I deactivated the account that was duplicated in Apple mail, unchecking the “Mail” and “Notes” checkboxes. This removed the duplicate mailbox inside mail. I still one one mailbox and it works fine.
On other macs where I haven’t don’t this I still have 2 duplicate mailboxes.
Everything seems to be working ok spam is still automatically filtered somehow and put into my Spam folder locally and removed from the server. However the ‘train as spam, train as good’ menu items and keyboard shortcuts don’t do anything now, when for example, I train as spam, in the past it would move the message to spam, now nothing happens.
Thanks for any advice.