Interestingly, it seems like Amadeus allows more than one passport on a PNR (even though AC’s websites don’t recognize more than one). Last year I had an AC/LX trip where I used a European passport outbound, and then my Canadian passport inbound. After I checked in with LX on the return, the LX/LH website showed BOTH passports on the PNR, whilst the AC site just showed the Canadian one (which was the last one).