No, Japan had already said they wouldn't send skaters to the first 3 events before the issues with France came up. Then they decided to not go to any of the events.I think the fairest system is to go by total points for the qualification to JGPF.
But I have a suspect feeling that they will simply re-assign Russian skaters results to events they were supposed to be at. Like Zhilina and Petrosian at Courchevel I, and maybe Akatieva and Samodelkina at Courchevel II. Which means those French podiums will change retrospecitvely.
And then they can have the normal point system.
Whatever they do, it's a shame the Japanese federation pulled out of the whole JGP, and I think they did that just because of the French debacle.