Hello Dayna,
You may want to consult your local CPA or Accounting manager for advice.
Since you received the funds back, I would simply void the duplicate payment in Payables. This will back out the AP and Cash accounts for the amounts that were originally booked. This will clear up the vendor and the GL for the payment. Then go into Bank Rec (Transactions | Financial | Bank transactions, and key a 'decrease adjustment' for the amount of the fee, using your cash account and whatever GL account you typically book 'bank fees' to.
(You may need to go to Cards |Financial | Account, select your account and mark 'allow transaction entry' to key the decrease adjustment. After posting this bank trx for the fee, then go back to the account and unmark the option again. )
Hope that helps.
Cheryl Waswick
Microsoft Dynamics GP Support