Thanks, is there a grace period between the end of family permit and waiting for the PR to go through?
I assume you mean the EU's Resident Card and not their 6th month Family Permit (entry to the UK)?
The EU rules are not like a UK "visa" where up to the visa end date means they are lawfully in the UK and after too if they have a valid application in, because they are protected under 3c of the UK's Immigration Act 1971. UK immigration laws and EU laws are not interchangeable.
These were the regulations you needed to follow -
https://www.gov.uk/government/publications/european-economic-area-nationals-qualified-personsUnder EU rules if you (her EEA citizen sponsor) is lawfully in the UK (following the EEA Regulations
at all times) then your wife is lawfully in the UK too.
For you to be lawfully in the UK you (the EEA citizen) must either be a Worker, Self Employed, Student or Self Sufficient "qualified person" and the last two requires you and your family members to have a Comprehensive Sickness Insurance each: or there is limited time for a Jobseeker. Or for you, the EEA citizen, to have the EU's PR instead of being a "qualified person".
PR is automatically achieved if you have been a "qualified person" for 5 continuous years in another EEA country.
As a spouse of an EEA citizen who is "qualified person" or who has PR in the UK, she is your Direct Family Member and therefore does not need an EU RC. Only your Extended Family Members need an RC. Your wife's RC was to show that she could work in the UK. An RC becomes invalid if their EEA citizen sponsor stops being a "qualified person".
https://www.gov.uk/apply-for-a-uk-residence-cardSo there is no "grace period" for a Direct Family Member as the EU does not have grace periods: either their EEA citizen sponsor is a "qualified person" or they are not; their EEA citizen sponsor has the EU's PR or they do not. The EU 2004 Directive does not allow a single day of not being a "qualified person" as that resets their '5 years to PR clock' back to zero; but the UK can be lenient on that and allow a few days.