I have been approached to assist in connection with a self-employed plumber, who also happens to be a qualified pilot.
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The pilot, the plane and VAT advice
There are a number of pitfalls here. Let's take input tax first: as the plumber bought the aircraft in his own name a couple of years ago, VAT on this and the repairs falls on him, not the company. From what you say, it couldn't now be argued that there was an intention for the company to own and manage the aircraft from the outset.
He would only be in a position to recover the VAT incurred if he sought registration for VAT, as a sole proprietor. If he asked for a current date, VAT on buying the plane can potentially be recovered (VAT General Regs. 1995, Regulation 111; goods on hand acquired not more than 3 years previously, services received not more than 6 months previously and not expended). If he asked for retrospective registration, yes, he'd have to account for VAT on his plumbing services, He might recover more VAT on the plane repair services, BUT - and it's a big one - in either case he would have to be able to demonstrate that the plane was acquired for and is being used for a business purpose. (I've not heard of a plumber needing a plane to get between workplaces or fly down a pipe, so I presume it would be a separate business activity to the plumbing). It sounds to me that the plumber, having acquired one plane, now thinks there might be a business; showing that he did say a year ago will be difficult.
To complicate matters further, I infer that there is private use of the plane, so any VAT claimed would have to be restricted to that part relating to the business use.
Given this he might like to ring-fence his current plane from the venture he's proposing, and develop that from scratch in the company.