i have gone through the WES process 3 times including my own evaluation as well as 2 of my friends. if the wes report says that so and so degree from ''non recognized'' university then even if the university is ugc approved they still wont accept it. do not mean to discourage you but just letting you know from my experience so that you get a clear answer
the above link gives you options as to how to contact them but i am not positive if they would take it into consideration ,but i guess no harm in trying