For flights between Japan and France you will get miles unless your are on a H, K, M, V, S, O, G or R booking class (so basicaly all eco classes except the expnsive Y and B).
Your BA operated BHD-CDG and CDH-HND flights will probably net zero mile, as per
https://www.flyingblue.fr/en/partner...ion?country=FR :
Earn Miles on flights marketed as Japan Airlines (JL) and operated by Japan Airlines, Air France or KLM, as per the earning scheme below.