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You can either raise a credit note for the difference - use this credit to clear the balance owing.
If it's a 'goodwill' write off, that's probably the easiest way.
Or, if it's a non-payment or unrecoverable, enter a Bad Debt journal to write off the balance.
If VAT is involved, there are certain rules around reclaiming following a bad debt ... see https://www.gov.uk/guidance/relief-from-vat-on-bad-debts-notice-70018
Hope this helps.
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