Because tags work across notebooks, you can go about this one of a couple of ways:
1. Pare down your notebooks and use them and sub-notebooks as additional organization filters.
2. Do what you suggest and create a new notebook, only bringing over the important items.
3. Move all notes to your default notebook.
You can’t delete all of your notebooks. You need to have at least one. To move notes, just select or shift-select/ctrl-select and drag notes to the new notebook. Dragging notes to “All Notebooks” will also move them into the default notebook.
Hope that helps!