@BethCrook ,
Updating the points probably isn't an easy thing. When you try to change the point values for a complete/incomplete assignment, Canvas gives a warning. Mine was worth 10 points and here's what happened when I tried to change it to 20 points.

That means that you would not only have to change all of the point values but the grades for all of the students. Writing a script to change the assignment points is doable relatively quickly (get a list of assignments, iterate through them and update the assignment to be worth 1 points and not count towards the final) but now you also need to update all student submissions for all of those assignments. Something that is definitely scriptable, but a very big change to the gradebook so you want to make sure you have it right and test it in beta instance.
It might be better to 1) uncheck all of the students who haven't turned in the assignment rather than marking it as incomplete or 2) use the missing grades feature.
Either one of them should keep it out of the gradebook. Then when they export the grades grade with the gradebook, they could use a COUNT function instead of a SUM function. Here's what the gradebook looks like when exported into Excel
In Canvas

In Excel (the notes are mine)

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