Hi,
Thank you very much for the details!
By default the plugin will not remove items, which does not have connection with the given taxonomy. To change that, turn off this option: https://i.imgur.com/qhcYij2.png
In your specific setup, I would also suggest changing the checkbox logic like so: https://i.imgur.com/EGBfZko.png
I beileve these should resolve the issues 🙂
