Dear Nandisha,
In the first place, I don't understand the logic behind placing an employee who has long been absent merely for the purpose of initiating DP against him for the misconduct of unauthorized absence. Suspension pending inquiry is an effective weapon in the hands of the employer to prevent the employee from meddling with the DP by way of tampering documentary evidence as well as influencing the witnesses by any means like threats, cajolery, etc. At times, some delinquent employees may resort to playing smarter by dragging the inquiry unnecessarily, taking advantage of their suspension. Therefore, suspension pending inquiry should be sparingly used only to expedite the D.P. and not as an empty formality or show of power. Once the employer exercises the option, whether knowingly or unknowingly, he has to diligently comply with the provision for the payment of subsistence allowance both time-wise and scale-wise. Any lapse in this regard can vitiate the entire D.P in case of judicial scrutiny later. Therefore, notwithstanding his subsequent resignation, you have to pay him subsistence allowance till his last date of service in the organization.
Normally, no prudent employer would accept the resignation submitted by a delinquent employee when the DP is in progress or final orders are pending. What I infer is that being satisfied with the voluntary exit of the unwanted employee, the employer has accepted his resignation despite the pending D.P. and hence closed it without any further action. Even then, I am of the opinion that you have to pay him the balance amount of subsistence allowance.