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I did. They all received their work permits without any issue. The only difference was that I had dropped a course in the January 2021 term. Since I had already completed the required courses, I dropped a non essential course since it was interfering with my research. The course showed up with the status "withdrawn" on my transcript. They had never taken up any additional course.
It is very odd. The course does not matter, as you said you already completed the required courses. It may be a misunderstanding. I don't know if you can do the flagpoling or not. But you can do a research on it, if you can go to border, you can easily explain and get your permit.
 
Do NOT flagpole if your permit was denied through IRCC. Plus you are out of status already soon, so you will probably get told to leave on your way there.
 
Do NOT flagpole if your permit was denied through IRCC. Plus you are out of status already soon, so you will probably get told to leave on your way there.
They will ask you to leave once you showed up at the border to do flagpole, so don't do it.