The universal principle is ignorance of the law is of no excuse. However, while a person lodged his letter of resignation, normally any HR shall enquire as to the reasons for resignation during which the benefits and/or disadvantages of going ahead with the resignation shall be discussed. It is a normal practice.
Now, what to do. You have to escalate the matter in HR itself to its highest authority like the HR Head(the ultimate authority). If you do not get any relief from the HR Head, escalate further to the Chairman level giving full details explaining how you were ignorant of the difference between VRS and Resignation and highlight the matter that you were not counselled at all in the matter (if it was a fact).
Lodge the request and hope for the best.