you have several documents from customs in your hand, on which ground you have claimed payment from bank. there is 5th copy of ARE-1, which is retained by yourself , duly signed by excise and customs both. make xerox of that copy and send to customs,
customs will mark on the copies " to be treated as original" and "to be treated as duplicate" after verification of the records at their end, also obtain a report from customs regarding the shipment taken place on the specific day under their EDI register.
submit the documents with department, .........to get the rebate claim you have to have good liason with department, and they will guide you time to time, the procedure and documents required to complete the file, otherwise they would push the file either to rejection on several grounds or pre refund audit. so keep chase up and back up with department atleast once in a week to track the status of your refund claim, as they will send the file to range to confirm the payment made genuine ness, and if needed the R/O will check the particulars with RG-1, and RG23A-Part2/PLA, then only send the file back to deputy commissioner.
better to discuss the issue with the technical superintendent, he will guide you with his best possible remedy, with shortest pain.