I found this thread because my wife has portal invite and I'm trying to figure out how long it will take.
As for your situation, I'm sorry to hear this. You should get some professional advice, but be prepared to start the PR process over again. The cohabitating rule with common-law is actually part of the immigration law. It is a hard requirement. The agent cannot take into account the medical emergencies and doctor's notes because that will not change that fact that you were not physically together in Canada...which is the law.
My wife and I knew about all of this before starting which is why we chose to get married quickly to start the process and understood we most likely may not be able to leave Canada during this time no matter what is happening in our home countries. Either that or forfeit. It is a hard and fast rule on the living together in Canada.