I've looked some more and the websites for both Canada and the US are unambiguous. They say that the Nexus is acceptable without a passport.
I called AS and after researching their manual the agent read exactly the same language as on the government websites except AS only mentioned travel to three cities in Canada, one of which is YVR.
Therefore AS policy is in agreement with government regulations at least for the route that matters to us. Given that agents are asking for passports when presented with a Nexus card the question remains what will happen at the gate if she either doesn't provide one or shows one that is expired.