Hmmn. I can see where that would be very annoying. I'd suggest next time this happens, download your activity log and contact Support - which, unless there's a major change, wont get you a quick response - but at least it gets the matter in their hands.
Meantime maybe tag your notes for their destination notebook as well as any other tags you might add - an emoji (🔸<name>) would make all the 'notebook' tags easy to find as a group, and then you could move the pre-processed notes in blocks rather than individually. Maybe.