How do I process a refund for a payment already presented on the bank reconciliation for a supplier payment that has bounced back or is being repaid?

Create a deposit in the Cash Book.
Go to Finance > General Ledger > Cash Book > Bank Charges & Credits
Select 'Bank Credit / Deposit', use the Suspense account.
This will DR Bank - CR Suspense.

Create an invoice in Supplier.
Go to Finance > Accounts Payable > Supplier Transactions > Invoices
Create a new invoice, use the Suspense account.
This will CR Suppliers Control Account - DR Suspense account.

Reprocess the payment to the supplier or, if not repaying the supplier, create a credit note to offset the original invoice.