I've done this many times - changing the departure city from Shanghai to Hong Kong and vice versa. Then again, I purchased directly from Emirates so im not sure if that makes a difference (it shouldn't really).

I would give Emirates another call and try to speak a different advisor. Give them your booking ref no and tell them you want to change to HK departure. You will get charged the £75/£150 change fee but there should be no fair difference (unless there is no availability in your class).