Are you looking to buy a new build? We are in the process of buying a new build and about to exchange contracts so this has come at a bad time for us. However our solicitor says it shouldn't be a problem and we can pay half the deposit, and pay the rest with the ISA bonus on completion. He said that none of his clients have lost out so far.
And to sparechange, we have over four grand in our help to buy ISAs, if we take that out to pay the deposit we will lose over a grand from the bonus which would make using the ISA completely useless. It's not that we don't have a spare grand but when we have taken the time to save that much in the ISA when you can only deposit 200 a month it seems highly unfair that we then won't be able to use it.
Both me and my partner, and quite a few of our friends have been shocked we can't use it for the initial deposit as they also have accounts. When we opened the account they said at the bank that this could be used for that purpose so it has been very misleading for us.