Just claim retroactive mileage as usual. When they do this manually, they should see that it was a paid fare and credit accordingly.
Although, I wonder whether they will give you problems because you upgraded using (I presume) OZ miles... they might argue that you should credit the miles to OZ. But I'm not aware of any rules that prohibit upgrading with one FFP and claiming the miles on another. Stand your ground if they try to push this upon you.