Sadly,
JetLagged hasn't given the OP the right information in response to their question.
Per 19.1 of the
QFF T&C's, top-up points can only be used towards the obtaining of what is defined as an award flight:
19.1 If Members do not have sufficient Points to redeem a particular Award Flight, they may purchase additional Points towards that Award Flight at the rates specified by Qantas,
Part 2 (Definitions) of the QFF T&C's defines an award flight as follows:
'Award Flight' means an Any Seat Award and/or a Classic Award, as applicable;
So in short, a plain text reading of the T&C's clearly states
a top-up cannot be used for the purpose of obtaining an upgrade from Y to J.
Now as to if QF's computing systems could track if the points are used to the award you state over the phone, I reasonably suspect they can - and I for one wouldn't like to be on the receiving end of a call from the QFF SC when they throw your account into a negative balance because you lied as to what the top-up was to be used for.
Some further advice on using top-ups:
Specific award in mind
It's important to emphasise that the points top-up can only be used if you have a specific award in mind which you are short of points for, hence the need to call the QFF SC to purchase the top-up.
Only request the top-up points if you are absolutely certain of what you want to the top-up for, and it's pretty much a done deal in terms of booking your flights. If you're teetering on the edge of uncertainty - then hold off until it's locked in.