not AF but I've had similar problem before crediting LAN flight to JAL. Flew on J class on its only domestic route with J class (SCL-IPC) but didn't get any credit on JAL as JAL only recognizes Y class on domestic flights, nevermind the D booking class and the long haul nature of the flight. Had no problem signing up for LANPASS and getting the full mileage, although couldn't reach JL diamond due to these segments being unrecognized for FOP.