I agree that this method of splitting purchase consideration into land value and construction value is unethical to certain but is not illegal, as you are getting title on undivided share of land, the sale value of which is based upon the stamp duty value. The rest is the cost of construction that goes to the builder as his revenue for his services. Now coming to your question, the property you are acquiring is an apartment, which comprises the undivided share of land and the cost of construction of the flat. Hence, your cost of acquisition of your property is the value as per the sale deed, evidencing the sale of land and the cost of construction as per the construction agreement. As and when you sell the property, the total cost will be considered as the cost of acquisition and the sale value in excess of such cost of acquisition, after indexation, will be your long term capital gains, if you sell it after 3 years from the date of your acquisition. So by executing the sale deed and the construction agreement, you will not lose anything.