To ensure that I'm on the same page, may I know if you're using QuickBooks Payments (Merchant Services)? If so, a disputed charge (also known as a chargeback) is recorded automatically on your Merchant Services Center. Our system will check for credits issued when a chargeback comes in, but on occasion, it will not be picked up automatically.
Additionally, once a merchant responds with a documentation of the chargeback, it can take up to 90 days to complete the refund cycle. It can sometimes take additional time for the following reasons:
The case is to be reviewed and processed.
Recourse to challenge.
If this shouldn't be refunded, I highly suggest contacting our Merchant Support team. They have tools that can pull up your account in a secure environment. They can also reverse the refund if you wish to.