This is quite relevant to me as well.
I am flying on Friday in J LHR-DXB-BKK returning a week later. Flights were booked via Emirates and are operated by QF LHR-DXB and EK DXB-BKK. I put in my BAEC number for the QF sectors and setup a new EK skywards account number for the DXB-BKK sectors. Will the QF flights credit TPs and Avios to my BAEC account?
Thanks,