How to skip a item in a EBS BAI2 file for which bank never received a check for it?

Hello Experts,

            I need an important help from you all. We have a scenario which is a follows,

Day 1: we receive a file with a line item for a payment to which the bank hasn't received check, and when we process it, it makes the entry unprocessed.

Day 2: we receive a file with the same line item and with check number for the payment and when we process it, it gets cleared while the line item we received in day 1 still says the same.

I would like to know if we can avoid the line item from making an unprocessed entry or is it possible to process it.

Thanks,

Rev