eBridge Connections has a really robust integration solution between Shopify and QuickBooks - which includes Refund integration so that you won't have to process them manually.
If you're interested in getting some more info, just email firstname.lastname@example.org.
Hope this helps! Cheers.
You can ditch Quickbooks! That would most certainly solve the problem haha. We use Xero and it integrates with Shopify to pull in orders, refunds, and Shopify fees. It is much easier to use that Quickbooks. I may be a little biased though since I work for a company that uses Xero. I am also a ProAdvisor for Quickbooks, but I refuse to work with them anymore because they are just so non-intuitive despite their company's name.
If you want to take a look at Xero, you can start a free trial here. Xero also offers a free conversion from Quickbooks in certain cases. If you decide you like it, you can get a discount on your first 9 months by contacting A4J here.