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HMRC internal manual

VAT Default Interest Manual

When to inhibit, amend or withdraw interest: Misappropriation of remittances

Where a remittance sent in payment of an assessment has been allocated incorrectly, for example to an earlier non-interest bearing debt, it can lead to continued assessments to further interest when they are not due. 

If this is the case you will need to correct the situation by arranging for the money to be re-appropriated. Appropriation policy is set out DMBM210100.