How to reduce the GR amount?

I have made the PO say for Qty1 for amount 1000 in FEB'09.

I made the GR for Qty 1 & amount 1000 in Feb'09

Vendor given us the invoice reduce price for amount 500..Accounts dept book the IR & release the check. then period has been rolled off. Now how can we make the GR amount to 500?

Pl advice..