Closure of Bill of Entry - Banking - Finance

We had made a payment to a company X in A country for import of certain goods in July 2024.The X company sent invoice for total amount that we paid and sent the products. The products were received by us making full payment to customs as per the total invoice value. But we had found one of the product not sent by X company and telephonically informed. Immediately he asked the Y company in B country to send the product as he was running short of the product and X in A country made payment to Y company in B Country. The Y company raised an invoice for the full amount of the missing product on our name and sent to us in India. In India we received as a normal shipment with the invoice value and we had made all the duty payments. Now this BOE is pending to be closed as the payment to Y company in B country is not paid by us. Kindly guide how can we close the BOE in Bank. The amount is around USD 5500.