I am not sure if this is a DIY builders scheme or a normal business development. First, in terms of new build vs conversion then if the original stables are demolished to ground level (or even with one remaining facade) then HMRC would usually see it as a new build. You may have issues if it is not capable of being sold separate to the existing dwelling. As such the construction work by the builder should be zero rated and the first sale of the major interest (freehold or long lease) would also be zero rated.
You mentioned it is being done within a separate entity. Is the intention this entity will then grant a major interest to the owner (as an individual rather than a limited company?). If so, then if this separate entity is VAT regstered, then I think they should be able to recover the VAT incurred on the new build (subject to the restrictions for certain white goods etc) as it would relate to the zero rated supply to a private individual. VAT notice 708 refers.
If it is being built outside the context of a business (as a private individual) then the DIY builders refund scheme should apply as it serves to put you in the same position as if you bought a new house (zero rated as above) from a developer.
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