VAT is already paid on full flat amount but later GST is paid

Hi, I had purchased flat in April 2017 and paid VAT of 1% on full amount of property cost during registration Since the property was under construction, builder had raised demand in which service tax was also included. Later GST was introduced , and builder has charged GST on the remaining amount. Also builder has charged 12% GST tax instead of 4.5% service which lead to increment in flat rate. Later he has given 5% of GST input credit so ultimately i need to pay (12-5-4.5)=1.5 % more than the previous agreed flat value. Also my VAT amount of 1% is not adjusted anywhere which was paid earlier on full flat value. Still my project is under construction in which 51% amount is charge with service tax and 49% is with GST. I have below queries on that: Is builder allowed to increase the flat value after introduction of GST? I have already paid VAT on 100% flat cost but since GST introduced later , I had paid remaining interest on GST in which VAT was not adjusted anywhere.. So am i getting cheated by builder or this is the correct way only..Please revert.