IMO, you should deal with CX. It is CX who will refund your miles, not JL.
There is no issue about refunding the difference between F and J.
The issue is whether CX should use historical prices or current prices. A similar issue would arise if it were a revenue ticket on CX metal.
You have to argue with CX that they should use historical prices.
Of course, CX needs to reissue the ticket and the higher rates for miles and surcharge will automatically apply. Hence, it is a goodwill gesture from CX , unless the case is mentioned somewhere in their T&Cs.