It's weird, I know this case doesn't apply to me but usually they give additional time for PCC submission, some members in this group didn't submit their FBI PCC as it takes months to get it and they all get extension for submitting it post AOR. I guess you met a very strict agent.
How it works is you need to re-create an EE profile and finish your job bank registration, and then email OINP office with new profile information and a very touching explanation regarding why you're rejected and why you won't be rejected again for the same reason to transfer your nomination from your old EE profile to the new one assuming by the time you email them, your pnp certificate is still valid. It takes them about 3 weeks to finish the transaction and give you additional 600 points again.