I flew JFK(YVR)HKG on a direct routing on an AONE3, but ended up with two boarding cards as there was a cock-up with the seat reservations and I had to switch seats in YVR. (In the end I got to keep my 1A, but that's another story)

IIRC, both boarding cards were taken at JFK when I boarded. I certainly didn't get off in YVR. The purser may have taken my YVR-HKG card on board, but it was late at night and I would have been in a champagne fugg.

Bottom Line: If you get two BC's, you shouldn't have a problem in YVR.