It was an upgrade both ways actually doing the following:
QFF number entered, upgrade request put through on outbound only.
Upgrade confirmed, changed to BAEC number.
Change to QFF number again prior to inbound, upgrade request put through.
Upgrade confirmed, changed to BAEC number.
All flights posted as expected to BA and points removed from QF. I would try to change it at checkin or the lounge and confirm it is changed at the gate personally, I have had a gate agent not change it correctly before. Hope it goes through for you.