Penalty on delayed possession of flat in group housing in Gurgaon

We have booked a flat as per the brochure and building & Floor plan provided to us in May 2008 with booking amount. Also paid 1 installment after 1st demand letter as per the booking agreement, but project didn't take off as some of the documents of builder not approved and it went till February 2010. So the further payment were stopped as no project take off. In Feb 2010 documents were cleared so we signed an agreement with identified flat no. and tower (BBA) with builder and paid down payment with in 60 days of the agreement signed as excavation started, means 95% of the payment paid as per the agreement in April 2010. In June we came to know that building plan was revised as 3 towers replaced in the place of 2 towers. Because of revised 3 towers adjacent original flat booked was impacted. So we thought of cancel the booking but we were offered by then GM sales of the company to choose a flat in another tower. so we identified a flat of the same floor size with same terms & conditions and written a letter to a builder company to attach all the amendments pertaining to 1st agreement to the new agreement dated July 2010 as this change in agreement date is due to change in revised plan of the builder.So the sole responsibility of this new agreement is on Builder not a buyer. Now at the time of possession, as the project delayed by another 2 years builder is calculation penalty as per new agreement. please advise