There is no mention in the post whether the employee went missing while on duty or otherwise. In the first place, in my opinion, the lapse of two years since going missing, the conclusion of the employer as revealed by the poster himself that this is a case of missing and not abscondence, and the issue of a non-traceability certificate by the Police upon a complaint lodged by the missing employee's family would indicate that there is no scope for any action by the employer under the CCS(CCA) Rules.
Secondly, as far as I am aware, there is no special law in India like the Presumption of Death Act, 2013 as in the United Kingdom. Therefore, if any remedy is available, it is only through the provisions of Section 108 of the Indian Evidence Act, 1872. However, it is time-consuming and has certain limitations for probate purposes.
While disposing of a writ petition filed by the legal heirs of a missing bus conductor employed in the State Transport Corporation, a Division Bench of the Honorable High Court of Madras has held that a person missing for a long period and not heard of for over seven years could be presumed to have died under Section 108 of the Indian Evidence Act, 1872, only on the day after the completion of seven years. The Court further observed that presuming the date from which a person went missing as the date of death poses inherent dangers because many claims that could be made by his legal heirs would become time-barred, despite the fact that the presumption of death can only be raised after 7 years from the date he was last heard of.
In this context, the Court cited Rule 49-A of the Tamil Nadu Pension Rules, 1972, which provides for the settlement of terminal benefits to legal heirs of missing Government employees on receipt of a "Not-traceable" certificate from the Police, subject to the submission of an indemnity bond that the payment made could be adjusted from dues payable to the Government servant if he later appeared and made any claim. The Court also noted that the logic behind such a rule is universally applicable.
The poster's establishment may consider this and take action to settle any terminal benefits accordingly.