Not sure if this helps, or is the issue, but  Once the refund receipt is completed, you have to match it with the refund receipt you’ve processed in Quickbooks.

1. On the left panel, click on Banking.
2. In the For Review tab, locate the refund.
3. Select the transaction, click on Find Match.
4. In the Match transactions page, choose the refund receipt.
5. Click on Save.

You may find this article handy in the future: How to Void or Refund a Credit Card Payment?