london uk flight with 2 hour transit in hong kong

hi. I am flying on Cathay Pacific to shanghai, but have to change planes in hong kong, still with the same airline. I will only be in hong kong for less than a 2 hour transit. Will this prevent me from being eligible for a 72/144 hour free transit in china? I am then in shanghai for 50 hours before the cruise leaves. This is so confusing as to whether the stop in Hong Kong spoils my chance of a free transit. Thankyou.