By entering into JDA, you have impliedly sold the land and the consideration for which is recieved in form of flats from the developer. This is why capital gains tax has to be paid on stamp duty value of the flats on the date of completion certificate recieved from CMDA less the cost of acquisition of the inherited property which is the cost to previous owner or fair market value as on 2001 if acquired prior to that.
This stamp duty value of flats (recieved under JDA) deemed as sale consideration would become your cost for computation of capital gains as and when you sell the flats.
To avoid incedence of tax on sale of flats, deduction can be obtained under section 54 by investing in another residential house. There is no requirement that residential house with same UDS has to be purchased.
Trust that above suffices.
Thanks and Regards
Lakshay