As part of the Daily Summary that MyWorks syncs to QuickBooks; any refunds issued in Shopify orders will be accurately included in a section of the QuickBooks journal entry.
An example of this is below, showing how the different details of the refund are also separated to their correct QuickBooks Accounts - which can all be set in MyWorks Sync > Settings.
The refunded payments to a QuickBooks Bank Account
The refunded product sales to an Income Account
Any refunded shipping to an Income Account
Any refunded tax to a Sales Tax Payable Account
Any refunded discounts to an Income Account
The COGS related to any refunded products - to the appropriate COGS and Inventory Asset Accounts
For QuickBooks companies outside the US, refunded tax is reversed under the same tax code as the sale instead of posting to the Sales Tax account - see Syncing VAT and GST tax codes in Daily Summaries.