It is probably just scarring of sorts. I have seen areas on crested geckos that were injuries that have already healed turn a red color like what you describe. I have specifically seen it on the crests of females, where the males bit them during breeding (but it didn't turn red until a few months after the fact). If the vet didn't see any signs of infection and the areas are healed up it is probably fine. Just keep an eye on it.