This is a valid concern and at the moment there isn't much active information available.
The CIC has released a statement
here but it seems to apply primarily for PR applicants of three countries: Republic of Korea, China and Iran. The crux of the matter is that you have to raise a web form from your GCKey account stating if you can/cannot travel before the COPR deadline and why not. They have said
"We’ll then give you more detailed instructions regarding restarting the processing of your permanent residence application. " which I think is unbelievably vague (do they mean reissue of a new COPR/one time Visa or the restart of the ENTIRE application process?)