It is common for the position of the vulva to change during your puppies growth. So while her vulva may appear recessed at this time it does not necessarily mean it will stay that way. Is there urine soiling or irritation of the area around the vulva or was this simply pointed out during the exam? If you can provide answers to my questions or possibly e-mail me a couple of photos I can provide a more complete answer. If your warranty covers congenital defects and corrective surgery were necessary it should be covered. You should notify your puppy provider of these findings.