An update - no issues boarding the plane in the US. When I got to customs in Canada (I don't have NEXUS), I explained my situation to the border agent. I had my cancelled work permit with me, and when he saw that he told me that I was fine to enter since the permit was still valid. This was not what the immigration agent told me when he signed the COPR and punched a hole through my work permit, but I didn't argue with the border agent. I guess I was a bit lucky, but the whole thing was pain-free overall. Thanks again everyone!