EU VAT

I have a UK based client who sells on the web both in the UK and EU and has warehouses in the EU from which EU customers are supplied on sales through Amazon. The EU vat is either paid by Amazon on behalf of the client or through a vat account the client has set up for the relevant country.  My client uses a 3rd party to export the Amazon EU sales to QuickBooks Online which creates invoices which include the EU vat which is shown as 20% vat although the vat amount is at the relevant rate for the country. As the EU vat has already been paid I am using an App to gross up the net amount, so the invoice reconciles with the payment, and reduce the vat to nil coded as no vat. No vat is, thus, payable to HMRC. However, the sales are then overstated and need reducing by the relevant EU vat rates which can be done by a journal between sales and the bank accounts from which the EU vat has been paid.

Is this the correct procedure or is there an alternative ?