I can't tell you for sure, but:
You are correct that as per IRCC's own former communications, your file should not have been closed. if you have to litigate your case, it shouldn't be difficult for a lawyer to overturn the closing of your file. but you'll probably never have to litigate it (see below).
I think the last email you received, where they state that your file will be permanently closed but can be reopened and reassessed if you reply within 10 days, is the latest standard email they send to people with expired CoPR. Most probably they changed their guidelines and wordings and some folks like you end up received contradictory emails. I myself received an email in July 2020 stating that my file would remain open if I am unwilling or unable to travel due to COVID. That was after I sent them a "not ready to travel" email as my COPR was expiring in August.
No one really knows what they mean by "reassessing" cases but my understanding is that they are talking about background check/police certificates and the medical visit.