You're going to be hit with a large-once off VAT bill.
You're taking it (the house) from a business-use to a perosnal-use (a 'self-supply') and are now liable to make good, what was in effect an interest-free loan from the Revenue to you.
the alternative would be for them to force you to sell the property. They may also start to charge you interest on the money. Revenue have plenty of options and you dont wont to get on the wrong side of them. You should consult an accountant/tax adviser before you proceed.
Will the amount of VAT to be repaid be restricted to the balance of VAT reclaimed less VAT accounted for on rental or would there also be VAT on the value of the house at date of deregistration?
That is the crux of the issue here - a very good question indeed. If he can deregister before selling the house - he'll only repay what he effectively owes.
Otherwise if he's to sell the house, he has to pay ALL the VAT which would be deemed to be included as part of the selling-price of the house!!!