Correcting J/E for Cheque reissued in Accounts Payable

Hi...I am having trouble reconciling my bank. 

I issued an extra payment to an invoice that did not exist with vendor. They pointed it out, i removed the invoice instead of reversing the payment. The cheque does not exist so therefore

1) Reissued cheque with correct invoices that were due.

2) Did a "Contra" for the total amount in AP and in cheque applied payment

So now in my bank I have the old "wrong" in my account. Affecting account US an AP, how can I remove wrong cheque #