Return trip with a third country in between ?

That route is so obviously ok.

Yes, your itinerary is definitely eligible for 144 hour visa free transit in Shanghai twice. In reality, you should present your itinerary as two travel legs:

Paris - Shanghai - Tokyo

Tokyo - Shanghai - Paris

In reality, when you have left Shanghai for Tokyo, your 144 hour visa free transit has terminated. After your landing in Tokyo, you will start a new one. This is very simple and used by many travelers.