Hello Rohith, 

I faced the same problem. The best thing to do if you miss class 11 is to get admitted to 11 again and then finish 12 and get your +2 certificate from a recognized board. This +2 certificate will be needed when you want to apply to almost any institution or course. Of course you can register with the NIOS board and directly give the 12th exam but it may become a problem in the future.  A lot of colleges and entrance exams do not accept NIOS scores. 

Hope this helps :)