accounts showing twice in unified folders

First, I have NO solution, but a suggestion: Sometimes unified folders needs a refresh. To do that, click help>troubleshootinginformation, scroll to 'profile folder' and click 'open folder'. Then, click the mail folder and (after shutting down thunderbird) deleting the folder named smart-mailboxes. On restart, thunderbird will repopulate the unified folders.

Another thought is that sometimes thunderbird assigns a folder, such as 'draft', but the account already had 'drafts.' If you see multiple folders like that, verify which is actualy used, and then unsubscribe from the other.