I'm going to go against the popular census here and argue Virgin America has no obligation to refund the fuel surcharge, regardless of whether they were refunded the YQ from Virgin Australia.
The fact of the matter is that the OP paid for the taxes and surcharge on the award ticket knowing that he was going to have to pay ~$2,000 in YQ. Both parties reached an agreement on the price as soon as the OP paid (or 24 hours after he paid, if we take into account the refund period). I don't see why the OP is entitled to a refund later on when the YQ charges are dropped.