Date of Resignation - employee applied for ESI leave for 3 months. after the ESI leave the employee decided to resign

Last ESI contribution period was March 2019 after that employee availed a maternity leave for 6 months and taken a long leave till 30 June 2020.

My dear friend after March 31, 2019 you were showing the employee on ESI Leave isn't it. You must filed the Half yearly return also for Apr - Sept 2019 as well as Oct 2019 - Mar 2020. Which means you have already shown her as employee till then. Now since she has officially tendered her resignation on June 30, 2020, you put that date as her last date of working to the best of my view.