A common scenario you can see is that a payment in a batch transfer is initially recognized by the bank later to be rejected and reversed. This can rejection can be apart of another batch even.

So to correctly reconcile this you go to the payment that is reconciled with the invoice that was reversed and then reverse the payment. This reversal will create an entry that you can use to reconcile against the bank statement line with the reversal. It will also reopen the invoices/bills associated by reversing the payment. 

The easiest way to find the entry quickly in reconciliation is to look for the partners with invoices reversed.

This scenario can be seen in various forms of batch payments including sepa.