open the profile folder in windows file manager. (the more troubleshooting information on the help menu contains a button to show the profile folder) open the the mail folder. Close Thunderbird so it is not running. Locate the "smart mailboxes" folder in the mail folder and delete it. Restart Thunderbird.

That will force a complete rebuild of the unified folders on restart.

This solution don't work. I delete the "smart mailboxes" folder but when I open Thunderbird it start to multiply the folders