I actually was in exactly this situation recently, flying YYC - YVR - SAN. My passport was in YVR. As a Canadian, I need a passport to fly to the US. I had checked in online, and as I had my passport information I was able to enter the data at check in. I was asked for a passport verification prior to boarding, I explained the situation to the gate attendant who simply put a note on the file, I collected my passport at YVR (had a friend bring it to the airport for me), I was asked again for a passport verification prior to boarding the SAN flight, I produced it - no issues.