Is it legally ok to have supplementary agreement against principal agreement for flat purchase ?

Dear Sir, I have purchase the 1BHK flat having 625 SQM area. The purchase agreement is done with the 625 SQM only. But when builder give me possession he disclose the details that he has reduced the flat area (terrace area) by 15 SQM because the portion of the terrace projection is affecting the building control rules i.e. the DCR therefore at the direction of the Town Planning Dept. the area of the terrace was required to be reduced by 15 Sq. Fts. I have accepted the same & builder has refunded the money of 15 SQM during possession to me due to which the agreement value is reduced by 46000. Now to correct it on paper legally builder is saying to have the supplementary agreement for reduced current area of 610 SQM against the principal agreement where we do not require to pay additional stamp duty. And the all other terms and condition of the Principal Agreement will remain unchanged and accepted by both the parties The supplementary agreement will be made on Rs. 500/- Stamp. Now the issues is I have purchase the flat as investment so is it ok to go for the supplementary agreement ? or Should I demand for the new revised agreement ? Will supplementary agreement create any issues while selling the flat in future ? Is there any other way to get it done legally ? Pl suggest me the right way to execute it out & to avoid any trouble in future.