Sorry - I should have added: On the online check in, it would let me check in for the return flight but not the HKG-PEK leg. Presumably for the same reason - that the reservation and the e-ticket has somehow become disconnected - hence my airport check in. The service counter (all three of them that were trying to fix my problem) confirmed that I was not the only person with the problem that morning and was because of the system upgrade.