It is an adjustment to your purchases.
To think of it another way you could have entered only the business travel cost when the vehicle cost were first entered throughout the year. To back it out at the end of a financial period you have to use the some tax codes and sale / purchase allocation as was used when the dater was over stated when initially entered.
Having said that, it really only effects your VAT returns as sales vat is offset against purchase VAT.
For more details see Private vehicle use - worked example