I have an hour-and-a-half layover at JFK and a ten-hour layover at CDG
Checking in at CDG? Do you mean obtaining my boarding pass(es)? I presume that AA will have checked me in for all of the legs that it can see on its system (perhaps FJ included), leaving me to collect at airports along the way only the boarding passes that it cannot print, but I'm not certain if the lack of an interline agreement between AF and FJ will preclude my bags from being checked all the way through to NAN, necessitating their collection and checking again at NRT. Strangely enough, don't interline agreements require the payment of monies/expenditure of monies handling the baggage of other airlines, etc.? If AF has told FJ that it won't do that for FJ anymore, then I would have thought that FJ wouldn't accept AF luggage in the absence of an interline agreement.
I'm not going to have to retrieve my luggage at CDG and manually transfer and recheck it again when I change terminals at CDG, am I? If so, then perhaps you are right; this may turn on whether NH and FJ have an interline agreement. Similarly, if I don't have to collect my luggage at CDG, it may turn on whether AA has an interline agreement with FJ. (I suspect that both AA and NH have interline agreements with FJ.)