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If you have not paid any of the VAT to Customs and you know your customer well enough, you might be able to sort it out between yourselves.
Any VAT errors under £2,000 can be quietly corrected on your next VAT return.
Otherwise, I agree with IP2 - give Customs a call. Try the National Advice Service first, on 0845 010 9000.
Nowadays Customs carry out VAT inspections less frequently. A well behaved small company can expect one visit every 5 to 10 years. For the best chance of avoiding inspections, just make sure that all VAT returns and payments are filed on time.
The only other way that the error would be picked up is by your accountant at the end of the year. If you have charged VAT but not paid it to Customs, and refuse to correct the error, then it will give him an accounting headache, and no-one wants that do they?
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