There are a few settings you can enable within QuickBooks Online that may cause issues with how Commerce Sync transfers sales information.
Automatically Apply Credits:
This setting will apply available credits to invoices under the same customer. If a payment somehow is unapplied, the next invoice Commerce Sync is creates gets this payment applied to it incorrectly. This causes the incorrect payment to be applied to the new invoice. This leaves a new payment unapplied, that will then apply to a future invoice within QuickBooks Online. This often causes a snowball effect that will apply the payments to the incorrect invoices for each date moving forward.
Enable Account Numbers:
This setting causes errors when you are first installing Commerce Sync, or when using the Sales by Category feature and have a new category. When we attempt to create a new item and account in QuickBooks Online, this setting will block the account creation, as Commerce Sync cannot determine which account number to use. Temporarily turning this feature off will allow our transfer to create the needed items/accounts for our mapping into QuickBooks Online.
In QuickBooks, go to the gear icon --> Account and Settings --> Advanced --> Automation. If you have errors related to this, turn the "Enable Account Numbers" setting to Off and go through the Fix and Retry steps in you Commerce Sync Dashboard: