I noticed this as well-he also doesn't have the burn mark at all throughout the whole Toy Story 2 as well. I don't know how Andy would repair it, but it looks like someone did.
Maybe Andy's mom or dad painted over it...in Toy Story 2 that's how the toy-shop guy removed Andy's name from Woody's shoe. Also, I think someone mentioned before that Disney (prolly Pixar as well) doesn't leave injury marks on characters very long, so as to not upset the kids.