I got a doctor's note for a lab report (it was over 30% so I couldn't MSAF), but even if I had MSAF'd, the procedure was to get an extension, but exactly when it would be handed in is something that I negotiated with the professor. I know another student who also had a doctor's note for the same report, but got a longer extension than I did...it wasn't a blanket policy, we worked it out with the prof based on our circumstances.
So in short, no one can answer your question except for your prof, and you should also check your course outline.
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