Hii!
If you have already passed class 12th and want to do it again through NIOS, then, you can give it. There's no problem in that. But, regarding the marksheets of the two, your CBSE marksheet will not become invalid, but obviously, you'll not be able to use or produce both of them simultaneously whenever required. The best out of the two will be considered for your future endeavours.
Hope this helps.
Good luck!