When your JFK-LHR upgrade was processed, AA should have provided you with a new eticket confirmation email with a new Baggage Information section. Did you receive that? What does it say about your baggage allowance? Those statements are quite clear about scope -- for example, it might say JFKLHR 2 checked bags or JFKCDG 2 checked bags. If the latter, it plainly encompasses your travel all the way to CDG.

As a practical matter, if you are on one ticket and one PNR, with a connection (not stopover, no overnight) in LHR, you'll check your bags at JFK all the way to CDG. So the JFK-LHR baggage allowance will apply.