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HMRC internal manual

VAT Accounting Manual

Accounting for VAT: payments of VAT claimed on returns: undisputed sums

Any sums that are not part of a dispute or enquiry should be repaid as soon as reasonably practical. You should not generally withhold payment of part of a claim which has been verified by you to be payable on the grounds that the rest of the claim has not been verified. However, where you have reason to doubt that any VAT credit arises at all, then there is no obligation to treat a part of the claim in isolation.