Hi,
As employee strength was just five, it was not necessary for you to register for PF Account. I assume that you have not deducted money from his salary towards PF. In such case you need not worry about PF claim.
With regard to the payment in lieu of 3 months Notice period, one need to review the clauses of the employment agreement, resignation letter, relieving letter and other related communication relating to his exit carefully to come to the conclusion.
You have to reply to his legal notice rebutting all his claims.
Regards,
Sandeep Hegde
Advocate
Platinum Legal