the seat will b alloted in general cateogery be clear while applying fo jee exam 

Since you might need to upload the soft copies of the original certificates and without them registration would stand  incomplete so i don't feel there's any option to go forward except as a general candidate(if u haven't completed your registrations yet). You may hope for extension of the deadlines for certificate upload.

Sumit you mean that you don't have OBC certificate in the format which college is asking or you don't have the certificate at all?

If you don't have the different format certificate but you have an original certificate then you can show your original certificate to them, they will allot you a seat in OBC category only and will give you an extension date for submitting the original certificate in the format they wanted.

But if you don't have the certificate at all then you won't be disqualified but will be allotted seat according to the general category rank.