@Manoranjan: Dear friend, please contact the D.I. directly and try to get an answer,if s/he is not satisfied with the previous application you may try to seek post- facto approval. Alternatively, you may file an RTI to know what decision was taken against your application for permission and if it goes against you, you have to move to the court. However, I don’t think your degree will be considered invalid ultimately. Hope for the best. Best of luck!