Service tax paid but invoice cancelled

Dear CA's,

Ours is NGO which runs on funds received from government. For getting reiumbursement we have to submit the bills / invoices against purchases made.

For purchase of materials in the month of october 12 we have filed reiumbersement, unfortunately we missed to submit bill of 1 material. Now when we are asking vendor to provide us the fresh invoice including previous payment, they are coming up with an excuse that service tax has been paid and thus invoice cannot be cancelled. 

I wanted to check what is the best possible solution so that we do not suffer loses.

Please suggest.