Dear Anubhav,
It is mandatory for each employee to receive the official communication that is issued to him/her. Refusing to accept the official communication is "misconduct". However, for refusal to accept the warning letter, you cannot issue second warning letter. What if the employee refuses to accept this warning letter also? Will you issue third warning letter? This cycle of issue of warning letter and refusal has to be nipped in bud at right away.
I recommend you suspending the employee immediately and issue the show cause notice for refusal to accept the warning letter. If he refused to accept the show cause notice also then let the suspension continue and order domestic enquiry. Based on the findings of the Enquiry Report, you may take the appropriate action. Possibly it could be termination.
However, before following these steps of progressive of discipline, I need to ask whether you have approved and certified Standing Orders? If the Standing Orders are not well in place then have you communicated to the employees that refusal to accept the official communication is also misconduct? Even if the certified Standing Orders are well in place, do the employees know that these are binding to them?
Above all, do you have sufficient evidence based on which the employee was issued the warning letter? Is it because HR received the call from HOD and HR jumped the guns? Have you investigated the matter thoroughly? When employee refuses to accept the warning letter this shows that his perceptions about alleged misconduct are different. Why this is so? Are you consistent in handling the indiscipline of the employees? Did you let off few defaulters earlier but not suddenly started invoking the rule of discipline?
There are so many questions associated with your post gentleman. Therefore, please give complete information.
Thanks,
Dinesh Divekar