Dear Aahna,
You have written that the employee has "left" the organisation and while leaving he did not hand over charge of his duties. Therefore, you wanted to send him the letter for the non-acceptance of the letter of resignation. Nevertheless, you have not mentioned whether the employee submitted his resignation or not.
The employee is at his/her liberty to cease the contract of employment nevertheless, he/she has to fulfil the terms and conditions mentioned in the appointment letter. Leaving the employment all of a sudden is nothing but abandonment of employment. Therefore, far from sending him a letter on non-acceptance of the letter of resignation, I recommend you sending him a letter on unauthorised absence. Inform him to join his duties immediately otherwise severe disciplinary action would be initiated against him.
If the employee fails to turn up for his duties then send him one more letter. If he still does not turn up then order the domestic enquiry. If he does not turn up for the enquiry also, give him one more chance to depose before the enquiry. If he still does not turn up then terminate his services. In case he was in possession of the company property then order one more enquiry to assess the value of the items held by him. Initiate proceedings to recover the amount from him.
Thanks,
Dinesh Divekar