No GUI used for any part of that? Entirely hand-made command line? Do you give a –dbpath?
If no dbpath, the database path is implied by the destination URL, so would object to leftovers.
GUI makes it easy. You can delete a backup, its database, and the destination data all at once.
For CLI, you deleted destination, but should delete either your --dbpath database, or find it in ~/.config/Duplicati/dbconfig.json which is a text file if you prefer to edit things carefully.
Another option is to bypass the lookup, abandon the old database, and set your own --dbpath.
Regardless, destination file contents and the local database that describes it must be matching.
If your goal is to “start over” with a backup, I think you only missed one step. After deleting all the remote files, you simply need to delete the local job sqlite database. The next time you run the job, Duplicati will see there is no local job database or any files on the remote side, so it will behave as if it’s the first backup.