Hello Kateallen, thanks for posting on the Community page, You should have VAT on the invoice and the credit note. The invoice will be a positive amount and the credit note a negative amount and they will cancel out to 0. It wouldn't duplicate the VAT at all.
Have you switched from accrual to cash?
It may look like it has, but when you switched, as long as you didn't set the effective start date for the new scheme incorrectly then there will have been an open transactions column that would have effectively removed any unpaid invoices and bills from the return amount.
