How to apply payment made last year to a bill revised and received in current year

Hi,

I am very much confused and need help. So we received an invoice from the vendor in 2021 and based on the instructions 50% deposit was paid last year with remaining 50% payable upon project completion. Before the project completion the invoice was revised in 2022 with a new amount and 50% was paid for that new amount invoice. Now they are asking for the balance payment not taking into consideration that we have already paid them deposit twice. How can I apply the deposit that I paid in 2021 to the new invoice that was received in 2022 so that my books shows the correct balance to be paid taking into account both the deposit balance.

Thank you.