To refund Money to your customer using Payment Voucher, the below are the recommended steps:
1. Create a Contra account then Issue a Debit Note, the journal should be :
DR Debtor CR Contra Account
2. Create a Payment Voucher DR Contra Account CR Bank
Note: in the end, the entries will be as:
After the Entries, You can go to Customer>Customer Knock off to Knock-off the DN and previous over payment (Receive Payment).