The only way I know of right now is to individually delete each note, which if you have very many highlights, isn't a workable solution.
I really wish they gave notebooks additional features, such as a checkbox to show if highlights from a notebook are active. Then I could turn on and off certain highlights. And then maybe you could delete a notebook and any highlights that aren't shared with other notebooks. Reportedly, they're working on some changes. I don't know what they are. We'll probably have to wait and see what happens.