I have wrongly charged VAT on a invoice for a new build home already paid, is there a way to show a refund of VAT on the second invoice, i have to issue the customer.

Hello there, @robsoncraig, 

Yes, you can create a credit note for the VAT amount that has been charged to your customer's previous invoice. This way, you can apply it to the second invoice. Here's how: 

1. Go to the Plus icon (+) at the upper right. 
2. Select Credit Note under Customers. 
3. Make sure No VAT is selected on the Amounts are field. 
4. Enter the customer name, date, products/service items, quantity and amount. 
5. Click Save and close.

Then, you can apply the credit note through Receive Payment. Here's how: 

1. Go to the Plus icon (+) at the upper right. 
2. Under Customers, choose Receive Payment.
3. Select the appropriate customer. 
4. Under Outstanding Transactions, first click the second invoice you've created. 
5. Under Credits, select the Credit Note.
6. Verify that the total pay amount is correct after applying the Credit Note.
7. Click Save and close.

You can check out this helpful article for more information: Enter and Apply a Credit Note or Refund to your Customer. 

This will get you in the right direction, @robsoncraig. 

I'll be here to help if you need further assistance. Have a great day.