Had the exact same thing just happen: JAL Haneda to LAX swapped out 777 to a 787. Originally booked F using American miles; now my seat is a J. Keeping it though.
I thought it would be as simple as automatically receiving a 20K mile refund (1st v. business on American's fixed partner chart), but when I called the AA rep said she needs to get in touch with a JAL liason and get back to me in 4 business days. Four days? Am I naive in thinking this is overcomplicated for what it is? Same date, same itinerary, same flight, just downgraded from an F to J.
The award gods hate me. This was my replacement flight after I cancelled an ANA flight also due to a plane swap; swapping me out of the "room" and onto their old business product.