Welcome to the QuickBooks Community, pd83. Please know that we aim to deliver customer satisfaction at all times that's why we fix an issue as soon as possible. With this, may I ask for further details on how you entered the refund and if you could provide me a screenshot on your end of which part of QuickBooks did you see the -$1000. I appreciate any additional information so I can share an accurate solution.
For now, I'm adding this article so you can view different steps on how to record a refund based on various scenarios: Record a customer refund in QuickBooks Online.
Please don't hesitate to click the Reply button below if you need additional assistance in managing customer transactions. I'm always here to help.