It doesn't hurt to ask. I don't see where you have anything to lose. If she refuses, I wouldn't think you would buy another Yorkie from her at full price anyway.
I would imagine though that if you had a contract it states on there somewhere that she doesn't guarantee size. That is pretty standard. The breeder I purchased from stated that she was positive mine wouldn't be over 2 pounds. Well she is 3 pounds at 5 months which is fine with me except for the fact that she charged me extra due to her size.
My vet doesn't believe she was the 10 weeks old that the breeder stated when I got her because of the progress of her teeth. It frightens me that breeders may be tempted to sell their pups earlier than ideal so that they can get more money for them because of their small size.