Similar thing happened with the Darkmoon Hatchling when that got hotfixed.
You have two options:
a) ticket a GM and ask super duper politely with sugar on top for a battle stone to upgrade the caged one (responses will vary).
b) accept it and wait a while - the Uncommon will become rarer than the Rare (I have both the Rare and Uncommon versions of the Darkmoon Hatchling
I personally would try a). If it succeeds, you can think about upgrading it to rare or not. Perhaps you might want to put the stone towards something else? Either way, you'll have options. If they say no, well, you're no worse off.