If you are on standard VAT accounting ...
Raise an Invoice on the supplier account to represent the repayment, it should be t9 and go to 9999. I expect it to be for the balance on the account.
Make a bank receipt T9 to 9999 being the refund from the supplier.
Go to the bank account and do a supplier payment of zero on the account and match off the "dummy invoice" refund to the earlier payment on account.
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