Just a quick update on this one. Contacted my BKK travel agent and explained the situation to her. She confirmed what many of you said - that UA had indeed taken over the booking and this was the reason it had disappeared from the master booking. She could still however see the updated UA flight in her systems where it was listed as confirmed. So it seems there is a limit to how much information checkmytrip can extract from your bookings, for some things you still need a proper TA!