After NDA came to power, it re-visited the matter. In 2014, Smriti Irani wrote to the Department of Personnel and Training (DoPT) to inquire whether Swamy's case falls under FR 54. Subsequently, DoPT clarified that IIT isn't bound by government's rules.
The matter will now be discussed at the next meeting of the Institute's Board of Governors (BoG), the highest decision-making body.
The ministry's latest letter asking IIT-Delhi to clarify its position carries more weight since it was issued with the approval of the HRD Minister Prakash Javadekar, also the IIT Council chairman. So, in all likelihood, IIT-Delhi might have to cough up Rs. 70L for Swamy.