The affected flights are:
As of October 4, JAL has received a total of 19,500 seat cancellations from tourist group according to Sankei (Japanese only). 9,200 of them are on flights departing from Japan while the remaining 10,300 are on flights departing from China. According to Mainichi (Japanese only), routes to mainland China accounts for 10% of JAL's international sales but a lot of the tourists have switched from JAL's mainland China flights to JAL's flights to Taiwan and Hong Kong. That helps lower the affect to JAL's business. ANA is facing similar increased cancellations and had announced extensions to their capacity cuts too.
Right now JAL has a special charges waiver policy (Japanese, English) in place for those who want to cancel or change their tickets on China-Japan routes. Only those who have issued the tickets on or before September 19 2012 are eligible.