There are so many pop-up windows : "Submit this notebook for grade "

Hey I just got one more idea. Click on the file where you will find all these notebook in a list form select all in the check box and then unselect only the required files for this assignment, and delete these notebook except one notebook.

here is a post link posted by @paulinpaloalto regarding getting a clean copy, updating and refreshing your work environment

I really hope it solves your problems. Otherwise let us know.
All the best!!!

Regards
DP