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Hello, I am Keith, one of the experts on Just Answer, and pleased to be able to help you with your question.
I am sorry to be so dense, but please explain what you mean by being not eligible to claim the VAT back, what VAT?
VAT Notice 708 states:
'Subcontractors are contractors who work to other contractors. For the most part they can zero-rate or reduce-rate their supplies according to the building being constructed or worked on'
Which makes me wonder up which which tree HMRC are barking. Your invoicing at zero rate appears, on the face of it, perfectly proper.