Dear Madhu, 

Your application would not be cancelled but you will be considered  as General Category Student.

And you will get Colleges at the time of Counseling on the basis of Common Rank List(CRL).

Therefore, you should try to submit the Certificate as it will help you very much. 

To know about the colleges that you will get, you can try Careers 360 College Predictor 

https://engineering.careers360.com/jee-main-college-predictor