Multiple notebooks in document view - how to work with them

In document mode, you can create different notebooks: each starts with a document clean of annotations.

You can move to study mode for each and it creates a new individual study notebook for that document notebook.

If you want to add a document to an existing study notebook, you can’t select an individual notebook, just the overall document. Furthermore, it appears to merge all annotations from the various document mode notebooks.

I was using separate notebooks in document mode because I have one large PDFs made up of several independent essays that I want to annotate separately and save under their own name. But then if I come to have one overall study notebook on the overarching topic, I hit the problem above when I try to add them.

As illustration, say my topic is X. I have one large PDF book that exists of several essays on X. Each is important in its own right, so I initially thought would like to annotate each under its own notebook name. I do this via document mode and rename appropriately when converting to study mode. All good so far.

But now I want to combine my notes into one study notebook for X. I open that study notebook and go to add a document but can’t indicate which notebook I want. So instead I chose the notebooks for the relevant essays and merge - but now when I go to document mode, all annotations have been merged into the one.

What is the thinking behind how to handle such cases, please?