Both QF and LH support having 2 FF numbers associated with a PNR -- one for status and one for earning miles. Unfortunately most agents (both QF and LH) don't know how to do that, but if you persist it can get done. The upgrade request is based on QFF status, while earning can be the LH/UA number (in the LH sector); so just be sure you don't change the status field but only the earning field and you'll be fine. If it is accidentally changed, then yes, you lose any hope of getting QF upgrade cleared (being QF bronze or lower).