If you are not seeing all of your expected invoices on the EC Intrastat Data - Despatches report please make sure that the Intratsat codes have not been set to be excluded from Intrastat reports.
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You can do this by doing the following:
Click Stock
Click Stocked Parts Menu
Click Stocked Parts Maintenance
Click on the Intrastat tab
Press F5 on the 'Def Transaction Code' column
Make sure that the tick box for 'Exclude From Intrastat?' has not been ticked
Click OK
