This looks like one of those stories you see on Facebook where a cat was super ugly and wouldn't get adopted, but then someone decides to rescue them. The cat is still ugly, but at least it has love. You can't give a cat plastic surgery, but you can give a stuffed animal plastic surgery. I guess in that case it's cloth surgery? I'm not sure how that works. I'd cut the eyeballs out and stitch them back the right way. All fixed.
Some would say to charge less for the defective item, but I say charge more. That's a rare piece. By economic law, it should cost more. Imagine if a Beanie Baby had a defect like that. It would probably score someone thousands of dollars. I'm assuming Beanie Babies are still valuable. If so, then I have a couple hundred dollars resting on my pillow.