Hi @JMW15
From an accounting point-of-view, the simplest way to do this would be to issue a credit note (with VAT) then re-invoice (zero rated) but I don't think that's how HMRC would want you to do it.
Strictly speaking, you need to hold evidence that it was in fact a new build. If you didn't have this from the customer at the time then invoicing with VAT was the correct thing to have done.
Speak to someone from HMRC VAT section. Ask the customer for their contact so that you're both speaking to the same person.
Ask their advice, step-by-step, and get it in writing before you do anything. This will ensure that you don't get stung further down the line.
Hope this helps.
