1. She needs to spend 730 days between 20 May 2016 and 20 May 2021 to be in compliance with her residency obligation. This is for the first five year period. After that, it becomes a rolling five-year period where they count backwards five years from the day you submit an application or get questioned about RO at a port of entry. In the first five year period they do look into the future - so if she returns in Sep 2020, they will consider that she will have ~8 more months added to her days in Canada. After the first five years are over, it becomes strictly retrospective - they will not consider any days in the future.
2. However, you are correct in thinking that she can return to Canada with a valid PR card, and if she is able to enter without being reported for RO violation, she can simply stay long enough to meet RO and then apply for PR card renewal. Since you will be applying after the first five year period, you will have to count backwards from the day you apply. So if you apply in Sep 2021, the five year period will be Sep 2016 - Sep 2021. If she has 730 days in the period, she will be compliant with RO. Note that you cannot count days before Sep 2016 - those will no longer be counted.
There is no requirement to have a valid PR card - you only need that if you are travelling. You can happily live in Canada with an expired PR card.
3. Now, as to whether she will be allowed in without questions about RO. This is just my opinion of course - but I think it's very likely that she will have no trouble. She has already stayed for at least a year, and the COVID-19 situation is completely unprecedented. IRCC has already made lots of new rules to help people affected by travel bans, so it's reasonable to think that she won't be asked any questions about missing RO. If you are well established in Canada, she has lived for a year (and will have ~8 months more counted), and you have kids here and show all signs of wanting to live here - CBSA takes all these factors into account.
4. As a PR, she has the right to enter Canada regardless of RO. CBSA (by law) cannot stop her. They can begin the proceedings to take away PR, but she has to be allowed in to the country. So you don't need to worry about being turned away at the border. Your absolute worst case scenario is that she will be allowed in and issued a report that tells her that they are starting the process of taking away her PR. Then, you have 30 days to file an appeal and fight it.