I did this exact thing last week. BA Gold in the booking, and used my QF Ltg account to upgrade - using the upgrade a family member facility. Only curious thing was I had to state my relationship to myself ;-) Otherwise both upgrades (lhr syd and Mel lhr) were processed at between 24 and 48 hours.

I would just leave the qf number out of the booking to save the challenge of what if the system refuses to let go of the at number and the points end up in the wrong place.

KF