Bill receivable paid manually

Hi

We have setup the system so that once the Bill receivable is remitted we can Create Settlement Batches to create a collection file to go to the bank

However what is the best way to treat the BR if the customer does not pay it so it is marked as Unpaid, but then the customer pays it later. So we want the receipt recognised, but we don't want the BR amount included in the next collection file to the bank

Thanks