Hi Basak. First of all, my heartiest congratulations for getting a good JEE Mains score. You have successfully passed one step of the IIT exam. 

Now, I would like to give you one good news: Hope is not lost!!! 

That is because, admissions to NITs take place on the basis of JEE Mains scores only. And that too, counselling only after the Advanced scores are released through the process of JoSSA. So, I definitely believe you will get the correct NIT depending on the score. 

For more, see here: https://engineering.careers360.com/articles/jee-main-counselling-seat-allotment

All the best! 

Dear Basak,

Counselling for IITs and NITs will be conducted combine through JoSSA.

You don't need to worry about this issue. 

You can check the counselling process from the given below link

https://engineering.careers360.com/articles/josaa-counselling

Good Luck!!