The whole airline industry is operating this way as the yield management software has become more capable and sophisticated. This is true for many different airlines, not just CX, and for paid tickets as well as awards. The concept is simple: market segmentation. It is a way for businesses to maximize their profit by taking advantage of various demand elasticities in different markets. Quite often an airline might have A-B-C available but refuse to sell B-C, for example. You ran into the same situation in reverse on CX, where they will do HKG-YVR and YVR-JFK but not HKG-JFK -- as they have issued the maximum number of awards for HKG-JFK that they want to issue in advance. CX usually releases such seats about a week before the flight date for award use, if they are still unsold. There is nothing that can be done about this, except to expect it to occur more and more frequently, on many different airlines.

As an aside, and you know this already (that is why you redeemed this type of award), but CX gets more for 2 awards HKG-YVR and YVR-JFK than they do for HKG-YVR-JFK. So the agent at CX doesn't have discretion to make this change after the number of award seats were determined by yield management; if they changed it, they are literally taking money out of the airline's pocket ... something they aren't authorized to do, just as they cannot negotiate fares and offer extra discounts on paid tickets. Only yield management can do that.