If you're seeing a Duplicate Document # error for your credit invoices in your QBO Errors page, there is a quick fix to clear them and get them synced over to QBO successfully.
What you'll want to do is go to your QBO integration page in Recurly (Integrations -> QuickBooks Online) and then click on Edit Settings.
From there, scroll down to Credit Memo Number Prefix and set a prefix there. Note that the prefix you set there MUST be different from your Invoice Number Prefix:
Make sure to Click Update Settings! You're all set.