Notebooks allow you to organize any "Parent" media (document, designation list, presentation) or part of that media, also called "Children" (pages, annotations, designations, presentation element) in any way you'd like. But this flexibility comes with a bit of a learning curve.
We've learned over the years that many users will logically assume that anything in a Notebook can be deleted from the Notebook without eliminating it from the database. This is true only when you understand how the program is thinking about the media in the Notebook.
The main thing to remember is "Don't Steal Children." This refers to "Parent" and "Child" media where the Parent can expand to show media related to it.
This image shows you what is Okay (checkmark) and NOT Okay to delete from a Notebook.
Notice that you can delete 2564.7 when it's in the Notebook independently, and not part of the larger, full document 2564.
Also notice the bottom annotation, 2564.1.1 which is okay to delete, but the annotations at the top of the image are not okay to delete and would be permanently gone if deleted.
The difference in each instance is, the Okay to Delete stuff is independently inside the Notebook and was not added as a child of the parent media. If you want only certain pages from a document inside a Notebook, only add those pages, don't add the full document and try to expand it and delete those you don't want, that's "stealing children" from the parent media.
If you're wondering the reason it works this way, it's because media inside of a Notebook is merely a shortcut to the original. If you have document 2564 in eight Notebooks, you don't have 9 copies of 2564. So if you edit one, by altering the pages inside of it, you don't have an errant 2564 conflicting with all the others. This is most important on Designation Lists and Presentations so you're allowed to work from within Notebooks and be confident that there's only one instance of the one you're working on.