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My guess is this that your anticipated refund is more than £10k so for this kind of repayment you need to submit Form 652. Please submit this form describing all errors and then request for refund from HMRC. Form link, https://public-online.hmrc.gov.uk/lc/content/xfaforms/profiles/forms.html?contentRoot=repository:///Applications/Vat_iForms/1.0/VAT652&template=VAT652.xdp
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