FolderFlags cannot be used to switch which folder Thunderbird thinks trashed messages should go to on an IMAP server. This is a separate preference; see http://kb.mozillazine.org/IMAP_Trash_folder for how to make the setting change. German users, if FolderFlags 1.1 does not work for you, please delete and re-install; there was a bug during the first 12 hours of its release in the German locale that has since been fixed.
View on GitHub at https://github.com/voccs/folderflags/