just simply call them by phone to your corresponding zonal iit, and tell them everything about it, they will suggest you the alternative, my two friends made a mistake of not attesting the 10th certifcate and they called iit kanpur(as per their zone), and they provided them with solution, so dont waste time and call them now!!!,

follow this link http://jee.iitm.ac.in/contact.htm

PS: if their any problem calling to ur zonal iit, call to the other zonal iit.....

No it won't be rejected if u have darkened the bubbles correctly..! Check out the prospectus..!~