Gst on work contract

"The bills passed have been deducted with 4% VAT on 31-03-17 and the payment is yet to be done."

All pending bills should be released without charging GST....... as VAT was already charged on the construction work....

The system is such that there is long gap between bill passed and actual payment released. The department has charged VAT on paper whereas the deducted vat is deposited when actual payment happens. Now the actual payment happens in say November 2017. So what should be done  to that payment as VAT would have cease to exist by then ? Should we deposit advance VAT on the bil ?