Yes, it is high time for you to escalate the matter to HO. You could have waited for three months and then itself you could have approached the higher authorities. In your application state the facts in chronological order.
The company has provided you the clearance. Clearance from the company shows that there are no dues with you. If any issue emerges after your exit, then current managers or authorities concerned should be competent to handle or solve the issue. It appears that someone at the higher authority does not want to solve the issue as it is considered as burden by him/her. Second interpretation of the incident is the lack of empowerment. Why the senior authorities are wary to solve the problem in their summary power?
General comments: - Four months after the exit of the employee, FnF is not cleared and this happens in MNC! I have often held in this forum that the gloss of MNC is always spurious. If the vendor submitted the bill four years ago and if it was misplaced then why vendor was not asked to provide the duplicate bill? Why this case lingered for such a long time? Persons working in these very MNCs have penchant to deride Indian companies as lala companies yet their work practices are no different!
So what is the actual issue here ? There a]must be some other problem or incident that you have not informed us about.
When you followed up, what was the reason given ?