I do believe the answer will lay, in what was happening with the vacant half, and what you propose to do with it. If it was available for lease, and this can be confirmed, ie advertising, sign, internet etc, and you are buying as a Landlord, and will be continuing to look for a tenant, then I understand that you purchased the whole as a going concern, and no GST should be payable. However if you intend to occupy, then there could be an arguement for GST to be apportioned. As I have not had this experience with a single title sale, I am not certain. If each portion has its own title, that would be clearer. I hope that helps, however get confirmation from a GST specialist accountant prior to signing the Contract.
This will depend whether the property is sold under the going concern provisions. If both vendor and purchaser are registered for GST and this is a going concern stated in the contract, no GST is collected at settlement, the Vendor does not pay anything in his BAS and the Purchaser does not claim a refund in its BAS.
If not a going concern, then provided Vendor is registered for GST, GST will be paid and then if the Purchaser is registered it can be claimed back.
The risk is with the Vendor if the ATO comes back and says it's not the sale of a going concern.