Is your query from a real-life situation or hypothetical? When was the charge sheet issued, and when did the person resign? Before absconding, was the person sincere and good at work? Did he have any serious personal difficulties (like illness to self/spouse/child, etc)?
If the charge sheet was for unauthorized absence and the person resigns after a long gap, as an employer, what more interest do you have in that person? You can accept and close the case unless he has some commitments to fulfill contractually/as per the terms of the Appointment order. Mentioning anything in the service certificate is a decision to be made by the Management.
Regards,
V. Raghunathan