The two sentences do go together, and are grammatical, but they would only occur in the particular circumstance of persistent enquiry.
Get a couple of notebooks from the pile on desk.
— There isn't a pile of books.
OK, just grab two notebooks.
— I can't see two notebooks.
Is there any notebook on the desk?
— No, there isn't any notebook. There are only sandwiches.
To find a context where "Is there any notebook on the desk?" and "There isn't any notebook" both work is not easy and ends up being quite contrived.
If the sentences are supposed to stand alone, as a spontaneous enquiry and its answer, then we wouldn't normally use any:
Is there a notebook on the desk? Can you get it for me?
— No, there's no notebook.
Any as a determiner usually indicates more than one object:
Are there any notebooks on the desk? I need one.
— No, there aren't any.