Vijay, when you registered for the JEE Advanced examination than at that time, you must have uploaded some of the OBC certificate and the OBC NCL certificate which you are not able to upload before 5th June must be the one in the prescribed format by the JEE committee but if I am not wrong you must be having an original OBC Certificate.

So, right now you can upload the original scanned copy of your OBC certificate and drop a mail to JEE Advanced official email address that you are not able to get OBC certificate copy in the prescribed format now but will definitely get it before admission. Later during your admission in any of the IIT, all your original documents are collected for verification. So, at that time you can show your this OBC-NCL certificate in the prescribed format.

It's better to upload your original certificate and drop a mail to JEE Advanced official website because it can definitely create problems. Most probably it will not restrict your results to be uploaded on 10th June still it's better to be on the safe side rather than indulging in problems later.

Feel free to ask if you have any more queries. All the best!!