Hi Ajay,
I am in a similar situation. I called the IRCC helpdesk - (1888 242 2100. Select options 2 then 3 then 2 again and select talk to a representative). I told the agent that I had missed the email and the deadline has passed (>40days). I asked if I need to start a new application. She told me that there is no need to start a new application for PR card. Just include an explanation letter explaining the reason for the delay and send it along with the photos and copy of email requesting the resubmission of photos. I have sent it on 12th June but haven't heard back yet.
Could you please share if you have any update from CIC regarding your case?