How can I do a "contra" on bank statement? Customer paid us same amount twice and was repaid by us?

You can create a cheque or expense to refund the overpayment, Marypillon121. This will reduce the bank balance and offset the customer's credit.

First, how to create a cheque or expense:

1. Click the New or Plus sign (+) icon.
2. Select either Cheque or Expense.
3. Click the Payee drop-down arrow, then select the customer.
4. Under Category, select Debtors.
5. Enter the amount, then click Save and close. 

Next, link the refund to the customer's open credit. Here's how:

1. Click the New or Plus sign (+) icon.
2. Select Receive payment.
3. Select the customer name.
4. Under Outstanding Transactions, select the Cheque or Expense.
5. Under Credits, select the Unapplied payment.
6. Click Save and close. 

When you check the register, you will see the refund. I'll include the screenshot to guide you better. 

I'll add the article about recording a customer refund depending on the scenario. 

We're here to fill you in if you have other questions. You can always leave a comment below.