Thank you for joining us in the QuickBooks Community. Allow me to share some information about syncing transactions from Shopify to QuickBooks Online.
I'd like to check this for you and get it taken care of myself. However, Intuit QuickBooks will provide support if your data have been successfully stored into QuickBooks using a third-party application.
All third-party application (non-intuit) will no longer have access to their software. You can check the Shopify's website for the detailed steps on how to sync your missing sales into QuickBooks. Or, you can give them a quick call so they can further assist you.