If your ticket allows changes for a fee, that is usually OK to just change one leg.
1. If your original fare conditions had a fee for a stopover in Tokyo you will have to pay that. And of course if your ticket did not allow a stop over you can't do anything.
2. It is not just the change fee. If the booking class you originally booked is no longer available, you will need to pay the fare difference up to the booking class that is available.
Rather than pondering, call JAL and ask what it will cost. And if it is even possible.