How can I create a VAT only Sales Invoice for missed VAT?

We can achieve this by creating two new candidate timesheets one as a negative amount without VAT and the other as a positive with VAT, with the resulting payment then for VAT only.  

Firstly you will also need to add a new Rate code called VAT Adjustment (optional)

Create a timesheet via the Incoming Timesheet Images area by clicking the 'Add new timesheet' button:

When you add the timesheet you need to select the relevant rate code, put the minus in the bill (the amount needs to be the net value of the invoice you need to add the VAT to) make sure in the bill Tax type it says 0% Gross - if you want to put an explanation in the description box this will populate onto the invoice. 

Next you need to create another timesheet this time as a positive including the VAT type you will need to tick the invoice without a timesheet image if you don't tick you will not be allowed to validate the timesheet. 

The 2 timesheets will now be sitting validated awaiting the invoice to be created

The invoice will look like this