I see this thread popped back up, apparently the bug’s still there.
Like Dawne said, I talked to someone in another topic a while after I made this one, there are a few solutions to the problem.
The easiest, and less extreme one, is to make your pet bathe in green goo in Maldraxxus. If however that doesn’t work for some reason, you can always ask a GM to restore your pet to you.