Ok folks, here's the tea:

- I took 3 BA flights in the last 4 days. 3 different bookings.
Every booking had the BA/Gold/Emerald number registered.

Flight 1: Changed from BA number to AA number upon leaving the lounge in LHR, with the lounge reception desk. New boarding pass issued with AA number and according status. -> Result: Points/Miles/Avios still got credited to BA instead of AA

Flight 2: Done online check in. Changed from BA number to AA number at check-in desk at the airport while checking in luggage. New boarding pass issued with AA number and according status. -> Result: Points/Miles/Avios still got credited to BA instead of AA

Flight 3: Not done online check in. Waited to check-in at counter at the airport. Gave the agent AA card to swipe; boarding pass issued with AA number and according status. -> Result: Points/Miles/Avios still got credited to BA instead of AA

So this can only mean one thing: Altea's Fly check in system is an Amadeus system. So is their reservation system. They are obviously connected somehow. The only logical explanation is that the FQTV number you wish to use (in case it is different to the one in the booking) has to be entered IN THE BOOKING and BEFORE CHECK IN. Otherwise you will not get your Points/Miles/Avios credited to the desired account.

Changing the number during or after check will do NOTHING for you.

So, for my upcoming flight, 21JUL16, I have had to call up BA to get the number changed in the booking. This HAS to trigger the miles to be credited to the wished account. If still not... I will really go bonkers lol