Dear student,

Yes you can go for the NIOS board for the improvement of the marks in mathematics even if you are in the 3rd year of the Engineering but it my contradict your studies for the semester exam of 5 semester.

If you completed class 12th mathematics from National Institute of Open Learning are surely eligible to take admission in regular engineering college. This is simply because NIOS is a recognized board. So, you don't need to worry about this at all.