I would definitely put a ticket in and speak with a game master.
I think the faction pets don't covert anymore when you faction change because you can have both horde and alliance pets in your Pet Journal regardless of what faction your toon is. You just can't summon the opposing faction pets.
The pets changed faction before when we could only have one or the other, but why convert an alliance Moonkin to a horde one when technically both can exist in a collection at the same time now, yenno? So the policy might have changed regarding faction switching, but only a GM can confirm that.
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, my vanity pet collecting blog!