Dear Sreevichin,
stamp duty for rectification deed will be calculated as follows:
Total Sq.ft x Guideline value (Present Value) minus Total Sq.ft x Guideline value (value at the time registration) x __% stamp duty as applicable to your State
Plus
Total Sq.ft x Guideline value (Present Value) minus Total Sq.ft x Guideline value (value at the time registration) x __% Registration as applicable to your State.
In the above case, you will be paying present value for 200 sq.ft which is to be rectified Plus Difference amount for 1000 sq.ft which you have written in the principal document.