Yep, I'm the OP :P

The offers did in fact reappear when I re-added my AA #. They also had appeared initially while there was no FF# at all. After I purchased the upgrade (one leg only) the second leg remained available for an instant upgrade. I was able to switch the FF# back to Qantas and the upgrade offer disappeared again. I was just worried nothing would bring them back and thought someone might have experience with this.

I'm guessing that this is an inadvertent result of AAs procedures to try to ensure that you can't use AA status benefits while crediting to another airline. Recent DPs made it sound like they were training reps to not allow that.