I also think that the agency was wrong. However, you may still run into trouble. The fact that the sectors showed up in your itinerary does not mean that you can check-in - hard to say. There are a few situations that will trigger a price change, even without a reissue, e.g:
* From a weekday to a weekend transpacific return - That will be a HKD400 charge (if they have not increased the price).
* Any flight to/from PVG/PEK about the end of July to end of August this year - the add-on sector cost is no longer applicable. The sector what is flown within that time will be charged at the regular fare.

My feeling is that the USD200 cost difference is the base fare difference between the regular fare (about USD250 one-way) and the add-on sector fare (USD50 one-way) before the surcharges.

I am not sure what is the best way to deal with it, but I have a feeling that the timing of your travel is the reason of the fare difference.