Thanks for the quick responses.

Sorry APIS?

On check in all info is correct.

This question is really for my parents, they have used the eTA and their passports together before, the only thing that is different is the email given for confirmation by Air Canada which I'm sure is not linking to the eTA.
The real problem is that the web check in is asking for a Permanent Residence Card details only, no other options, and entering the eTA info in lieu of a PR doesn't work.

I have told them not to worry (I'm in Canada they are in UK) but deal with it at the airport, but my Mum is a nervous flyer at best and I though if I could get a nice neat answer I might be able to calm her down!

Thanks again