Well, I'm no expert on VAt or tax assessments, but I do know (because I've been advocating it for years) that if HMRC want, they can simply raise a tax assessment to a company, and they then must pay that, they can appeal it if they want, but they still must pay in the first place. I can't see why they don't do that to force the Starbucks and Vodafones of this world to cough up.
Anyhoo, if its like that, then you have to pay up, even if you appeal, although the sporting thing would be for HMRC to wait and see. They don't have a big rep for being sporting.