Thanks everyone. If we knock it all down and do a new build to get the zero rated VAT we will need to do retrospective PP for a new build as we can't afford to stop work until PP comes through. There is a risk with that as we may not get PP although the risk is very small - it's a residential street with lots of different types of houses on it and we would be building exactly the same house as we have PP for but just doing it as a new build. I don't think the council would have much chance in an appeal with that.
However, there are additional costs with a new build so I think it will end up costing us the same, if not more. Also, as work has already started we have already paid VAT for a considerable amount of the work which will be unrecoverable and until we have PP for a new build (at least 8 weeks) any work carried out could be deemed by the HMRC to have happened before it was lawful. Even if the builder doesn't charge us VAT, if the HMRC come after him, he will come after us for it, which we can't risk.
I think we'll keep a couple of walls and not do the new build.