If you have incorrect VAT values on your VAT Return due to transactions missing from the report, please check the following:

• VAT Basis in your settings, dates of your invoices (and dates of the allocated receipts/payments if on cash basis)Issues with VAT Control and Country SettingsA major reason for differences between the VAT control account and the VAT report can be the VAT basis used (e.g., cash vs. invoice basis).
• The country of the contact, Discrepancies may also arise from incorrect country settings for suppliers; verify that the correct country is selected to ensure transactions appear correctly on VAT returns. Changing supplier's country post-entries does not affect existing invoices directly but can change how transactions are reported.

• The VAT rate that has been used on the transactions. 

   

  The above should help clarify why specific transactions are not appearing on the VAT Return. You will need to delete the VAT return (once it has not been submitted yet) and re-run the VAT Return to get updated values after making changes.