I eventually gave up trying to do this; it is possible to change only a single segment, but the default is to change the FF# for all segments being checked in. Less than 1% of agents know how to do it right and all segments wind up being changed. And if you change it later, it backdates; so if you change LAX-LHR-NRT to QF and then change LHR-NRT to AA it will often cause LAX-LHR to also change to AA. I'd suggesting living with it all accrued to QFF ... or put NO number into the booking (but then you lose out on opup status) and put the boarding pass through for credit later. There just isnt a good solution for this, short of learning the keystrokes on how to do it for a single segment change (different on each airline, though I did learn it for AA and BA and CX at one point, but have forgotten it as I no longer care to do this).