The magic word could be 'reissue the ticket and clean up the record'. The agent can remove the TK (or HK?) segments on the AA side, but whether the change will propagate to JAL is unclear. On JAL/Amadeus, the AA legs are probably listed as Info Segments (not active/live) anyway, so however it appears doesn't really matter.

Not sure if the effort is worth it though. If the JAL flight has not changed, and there is no double booking on JAL, and you have a seat on JAL that you like, the purpose is mostly to be able to view the reservation on the JAL website