Sales tax tds

A Company has entered into contract with a builder for their new factory. The major raw material was supplied by the company. the contract has now crossed 2 years and is in stage of completion. Payments to the contractor was made as certified by architects on running bill. Since the contractor agreed to give form S no sales tax TDS was recovered. But the contractor has not given form S and now says he cannot give form S. The final bill is pending for payment. What is the liability of the company. How much to recover and pay now.