You can deduct the business use of the vehicle if you use the standard mileage allowance. Since the reimbursement was reported on your 1099-MISC form, you need to deduct the cost of using the vehicle to avoid being taxed on income you didn't receive.
If you sell the vehicle, you will need to determine what the depreciation equivalent deduction is for it, which simply entails multiplying a rate by the number of miles you used to get your mileage deduction over the years. If the sale amount is nominal, you can choose to report the basis of the vehicle as zero, and treat the full sale as taxable, to save you some accounting work.
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