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They most likely saw your previous visa refusal but thought it was insufficient to deny a PR application. Several reasons may have played on in the visa officer's head before they decided not to take it up against you.

Due to the COVID-19 pandemic, international travel in my country was banned. I was not able to land in Canada and my COPR expired.

International flights here restarted and I applied for a COPR extension. Can IRCC go through my file again and see if there was any overlooked misrepresentation?
 
Due to the COVID-19 pandemic, international travel in my country was banned. I was not able to land in Canada and my COPR expired.

International flights here restarted and I applied for a COPR extension. Can IRCC go through my file again and see if there was any overlooked misrepresentation?
Very unlikely that they would start looking at your initial application forms to see if there was any inconsistency. To issue an extension of COPR, the officer would most likely take a look at the notes of the visa officer who approved the PR application
 
Very unlikely that they would start looking at your initial application forms to see if there was any inconsistency. To issue an extension of COPR, the officer would most likely take a look at the notes of the visa officer who approved the PR application

During my landing, if they ask me that question about having been denied admission and I tell the truth "yes", what's the worst that can happen?
 
Not sure they ask this question during landing. I can’t remember being asked that question myself. However, if they ask, you just reply that you have never been denied entry but has been refused a visa application to Canada before