I had the same issue. Had DFW-TYO stop TYO-Jakarta. Then a Cathay Return. Tried to change online to ORD-TYO stop TYO-Jakarta then SIN-TYO stop ORD. Got to the end and failed. Called they couldn't change it either.

Then i just rebooked that itinerary from scratch and it worked. Called back in and had them cancel original. Also got the partner fee refunded so i didn't have to pay that twice. Appears to be an IT issue.