After repeated reading, I have found the following:
1) The employee's joining date is June 4, 2018.
2) The employee is continuing and paying contributions.
3) HR has processed the exit of the employee on June 5, 2018.
Under this situation, the record is destroyed, and the contribution itself is reduced to 1 day as HR has processed the exit on the very next day. Therefore, the only procedure is to quickly go to EPFO and request them to cancel the generated exit.