Did you apply for leave under proper acknowledgment?
Did you inform leave by phone,SMS,email, in person, by letter thru normal post?
First of all submit a written communication narrating all previous communications that on dated...............you informed by phone call/normal post etc to Mr/Ms.............that you shall be on leave from dated...........to dated...........and requested to extend the leave..............from dated...........to dated.....................and leave was approved during conversation etc and lawyas kept the establishment infrmed...........................and have not basconded at all.
Thereafter you have the option to submit notice of resignation (under proper acknowledgment), preferably after joining the service and submitting leave application under proper acknowledgment..................for the period you were out of office and narrate all previous representatios in leave application also.........................
You may seek help of elders in the family, employee's/IT-ITeS employee's unions/Trade Unions leaders, labor law consultant etc to draft your communications and build favorable written record.