Hi,
Considering that the flat was taken for the benefit of capital gain, it is advisable not to surrender the flat. Although department may litigate your exemption claim whether you surrender or not but the chances of your winning are higher if you don't surrender the flat.
Further, if you surrender it, interest will be taxable as other income and not as capital gain.
Please feel free to call/ revert in case you need more clarity.
Thanks and regards
Abhishek Dugar
CA CS B.Com