we landed from KIX, and having a cruise in 2 days…back to Japan. GOt our 144 transit visa! But what

Daryaa, it is logical that you were not be able to get 144 or 24 hour visa free transit by having an itinerary:

Japan - Shanghai - Japan

As you can see, this is a round trip ticket and not a transit, so a lady that told you that you need a ticket for a third country was absolutely correct. It is also logical that you were granted a visa free transit in Shanghai since you have presented a ticket for Hong Kong.

Now, I do not properly understand what agent cancelled your tickets and what tickets your are talking about? If I understand properly, you do not intend to proceed to Hong Kong and instead you plan to join the cruise that will return you to Japan? If I am correct, you are performing a breach of rules and you may be denied boarding. Also, you could be fined and after that allowed to board a cruise with some remark stamped in your passport that will prevent you from entering and/or performing visa free transit in China for a certain period.

In any case, you were really supposed to proceed to Hong Kong and to immediately return from Hong Kong to Shanghai in order to catch your cruise to Japan. You cannot manipulate with the basic rules of visa free transit because the Chinese side will definitely react and some consequences will be inevitable.