You're on the right path with creating a refund receipt, Andrea. Here’s some information to help you through the process.
Since you’ve already processed the refund through the Merchant Services account, making a refund receipt will help keep your records accurate. Keep in mind that the payment methods shown in the drop-down are for customer preference only.
Then, you've mentioned that the account is already added to the Chart of Accounts and a prompt message is appearing, stating that the account is already in use, you can sign out and sign back in to your QBO account to refresh the web page.
Once you're logged in, create the refund receipt again. If the account still doesn't appear in the Refund from drop-down menu, I suggest contacting our Live Support team. They can look into this further and assist you in creating the refund receipt seamlessly.
If you have additional questions regarding customer refunds, please feel free to reach out again. We're here to assist you.