Yes, Don't be worried about it. JEE will accept your passing certificate of NIOS board examination if you are appearing for NIOS On-demand examinations to improve your marks in 12th Board. The other certificates like Migration certificate and Transfer certificate will be provided by your school authorities where you were registered for 12th Standard (UP Board) and these documents will have to submit as they are (without any changes).

If you still have any doubt regarding this, do let know through comment section.

For any information regarding counseling, cutoffs, etc.. you can use the B.Tech companion from the link given below:

https://www.careers360.com/btech-companion