Hello there, Stefano. Please note that QuickBooks Online (QBO) relies entirely on the data that Shopify sends over. If any transactions are missing, it could mean that they have not been sent from Shopify yet, or they are being held back because the order is still marked as pending or unfulfilled.
We recommend reaching out to Shopify support to review why these specific transactions are not being exported to QuickBooks. They can check if there is a sync error on their end or if certain order types are being excluded from the data feed.
Regarding the GST/HST exceptions, you can double-check your settings in the Shopify Connector app within QuickBooks by going to the Tax Mapping section and ensuring your Shopify tax codes match the correct tax agency and rates in QuickBooks. This will help keep everything in sync.
These exceptions happen when a tax rate is recently changed or a new tax code is added in Shopify. When this occurs, the connector gets confused and flags those transactions as exceptions because it does not know where to send the money. By properly matching the tax codes in the settings, this issue will be resolved.
If you have further questions or concerns, feel free to leave a comment below.
