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Hi. My name is*****'m looking at your question now and will post my answer or ask for more information here in a short while.
You can choose not to reclaim the VAT if your business mileage is low as you can read under Fuel costs here. You don't have to formally opt out so far as I'm aware.
In your self-assessment claim the VAT inclusive cost of the fuel used on business as an expense or use the mileage allowance rules. You can use these if you are self-employed.
I hope this helps but let me know if you have any further questions.
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