The simplest and most direct "fix" is to brut force delete the stuff and force it to be recreated. Goto the More troubleshooting information on the help menu Click on the show button for the profile. Close Thunderbird. It must not be running for the next step, even in the background. In the file explorer windows that opened from the troubleshooting information. Open the mail folder. It will show a folder called "smart mailboxes", delete the folder (Perhaps move it to your desktop in case this messes up and then delete it) Start Thunderbird. In the absence of that folder Thunderbird will recreate the whole smart mailboxes thing and regenerate the listings as it starts up. So startup will be slower than normal.