1) What Builder will be benefited from your sales deed, the property which is already sold to you which was belong to him.
2) Keeping agreement copy with him for his safety, because property is still on your name.
3) If you have any fear regarding he will not refund your stamp duty money etc, you can make affidavit that sales deed is hand over to builder and on cancellation of deed he is going to hand over refund of stamp duty amount.
4) There is no hard and fast rule or law who will keep the sale agreement for cancellation purpose, actually you are returning property to builder again, How builder kept trust on you with out paying full amount sold property on your name.