The nature of your transaction can be properly ascertained only after seeing the agreements. The answer to your query may not be correct based upon the information given by you.
Based upon what you stated, it appears that you acquired rights for allocation of x sft of land and not for the land itself.
It appears that the cost of acquisition is for x sq.ft of land. As only (x-y) is registered, your right to receive the x sft of land is converted into acquisition of land. So when the land is registered in your name, there is capital gain on extinguishment of your right to receive x sft of land.
Now in lieu of allotment of land, you received proportionate return for less allocation of land. Further you have received return to match market rate of land and additional amount for the delay. All this will be part of consideration you have received for the extinguishment of your right to receive y sft. Capital gains will have to be ascertained on this basis.
Even if you have received the amount in 2 financial years, the date on which the extinguishment of your right takes place will be the date on which your capital gains arises.
