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Quickbooks FRS VAT return and the reverse charge?

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I have a client who is on the flat rate scheme for VAT and we use Quickbooks online for his records. Although he is on the flat rate scheme he is charged fees by Amazon for sales which are subject to the reverse charge and these should still be included on the VAT return. The VAT should be included in boxes 1 and 4 and the cost value in boxes 6 and 7. None of the reverse charge VAT codes available in QB apply this correctly to the VAT return and Quickbooks have not been much help. Has anyone else come across this problem and what was the outcome?

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