Visa application and 144-hour visa-free transit question

Yes, your entire itinerary is definitely eligible for 144 hour visa free transit twice. You should just keep in mind that you are not allowed to have any additional landing (stop) within mainland China of any kind beside the cities you have mentioned. I am telling you this because I am not aware that Chongqing airport has a direct flights connecting it with Tokyo. I know that Hainan Airlines will resume direct Paris flight by the end of November, but I am not aware of any flight to Tokyo. Please, re-check your flight itinerary because it would be pity to be stopped at some point because of a detail that will make you ineligible for this visa free transit scheme.

Xie xie ni for your answer. Yes I have been having trouble finding connecting flights, I might skip Chongqing and return via Beijing, it is OK to visit twice so close in time I assume. Many thanks for the Hainan Airlines tip, I will check their web site for flights. One last question, is it OK to have a flight out of Beijing with a different airline than that I arrived with? Will this cause a visa issue?

Don't worry, it is okay to use it twice and there is no problem of taking different airlines.