Just to update what actually happened. Here in Hong Kong, airport control happens quite early as you can check in at Airport Express station the calendar day before. So I called Reservation to explain the situation, and the person explained that seats should have been reserved/locked up once step up has been confirmed, but Airport has control of assigning seats by the time the step up has been confirmed and there is nothing she could do. She called Airport Control and got it sorted, and then I was able to go back to online checkin and print my boarding passes.