Capital Gain Tax in Joint Venture Property Dealing

Dear Sir, I had a plot which I gave it to a builder in JV ..Now the builder would construct 8 flats on it in total 4 floors, whereby he would keep 5 flats and I would get 3 flats . I would get 1 flat on 1st floor and 2 flats and 2nd floor . Now I want to retain both flats of fourth floor and use it as one residential property as I have a large family and want to dispose or sell off my 1st floor flat .. Land Value as per RR Rate of the land is around 1 crore so I belive in JV since half flats on land would be with builder capital gain would be for me on 50 lakhs . Now value of 1 flat as per RR rate is also 50 laks and since Il be converting 2 flats as one ,value of flats would be 1 crore . So now question is since the agreement happened on September 2016,should I while filing returns mention that against this capital gain I have reinvested the amount in this flat. What proof do I need to submit to IT Department . What happens when I sell off my 1st floor flat .How would tax be calculated on it .Lastly I already have a ancestral flat on my name where I am currently living ,can I still take benefit of Section 54.