I appreciate you posting here in the Community, Jyoung-teamlogic. Let me share some information about the Autotask invoice transfers to QuickBooks Online (QBO).
When integrating data on the invoices from Autotask, QuickBooks only depends on the information stated and provided in the Autotask app. Let's ensure these are in complete detail before integrating or transferring them into QBO.
Also, to ensure you've got the right information on how Autotask integrates data to QBO, I'd suggest contacting Autotask Integration support. This way, they can check the details and further provide you with the procedures to help resolve the issue.
Moreover, you can visit this link to guide you with other QuickBooks tasks that you may utilize in the future: Help articles for QuickBooks Online.
Don't hesitate to let me know if there's anything else I can do to help. I want to make sure you're taken care of. Have a great day.