If you encounter issues when running the VAT Return report (VAT 100), specifically where VAT refunds or VAT payments you've entered are incorrectly included in the return, it may be that the incorrect VAT rate has been used when adding the transaction.
Check the receipt (or payment) transaction to make sure you used the VAT type R: Refund, and that the net is showing as £0.00. Select the three dots and 'Edit' to review the details, make any necessary corrections, and then save the changes.
You can re-run the VAT 100 and the figures will update to exclude any prior VAT refunds or VAT payments.
We do recommend reviewing the VAT List before submitting a VAT return, to ensure receipts and payments have been entered against the correct VAT rate.