Any pending enquiry against you doesn't give them a licence to with hold your pending dues leave encashment and gratuity by your ex employer.
So, you should serve legal notice to employee asking him to clear your full and final settlement as well as other pending dues within 15 days of the receipt of the legal notice.
If he fails to adhere, you can file a suit for recovery under the Order 37 of the code of civil procedure for recovery of money.
If the amount of gratuity is also not paid by the employer within the prescribed time of 30 days to you, you have the right to file a complaint to the Controlling Authority under the Payment of Gratuity Act within the area where the employer’s establishment is situated or where you were working at the time of termination.
Feel free to call.