It is questionable whether there will be a 'clawback' by HMRC of the VAT that you didn't pay. On one hand, the business of renting out the property did not continue after you bought it, so it is hard to argue that this is a transfer of a going concern (TOGC). On the other hand, you intended to continue to rent out the property and it was only because of circumstances beyond your control (i.e. the tenant moved out) that you didn't continue to rent out. But there is a further point to note. If you look at VAT Public Notice 742A (at section 3.2) you can see that there is an exemption from VAT if the previously commercial building is adapted to use as a dwelling. This may be relevant to your scenario. I would advise you to write to HMRC in Southend-on-Sea to ask for a written ruling.