I did YVR-JFK-HKG on CX (where the JFK-HKG flight was CX 889 and it stopped in YVR, but ticketed as JFK-HKG) and didn't have any problems.
I guess as long as the "stop" is not printed on the ticket then it would be ok.
(Note: YVR-JFK-YVR-HKG is not allowed)