@YimBones -
Yes select the does not count towards final grade box for the assignment.
If you are still worried about it, just create the assignment where the upload is to occur and make it worth 0 points and click on the box does not count towards final grade box. That way students can upload to the assignment, and there is no score that will be reported - of course you could use the set default grade option.
I wrote the above and then re-read your message and went and tried out something in my playground. I Would select the does not count in final grade box, make the assignment grading complete or incomplete and make the assignment worth 0 points. Then after the submission deadline you will just need to mark the students with no submission as incomplete. Then you can use the set default grade to complete to apply to all the ungraded submissions.
Ron
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