DIR 11 filed without intimating the company

In your case, company will not be liable if company never received any resignation letter. As you said director informed the company then he informed through speed post, email or by hand. You can prove it through that. if you can get DIR -11 copy then check was the director selected any mode in case of information. You have need not worry, once you satisfied then file DIR 12 with late fees and pass the resolution in the Board meeting held after receiving resignation letter.

Resignation letter is received by the company through email.. But d problem is director has filed his resignation 3 yrs. Back dated. In mca master data it's showing d name of the director with begin dt. And end date.. When can Co. Appoint new director to comply with the provision of 2 directors in pvt. Co.?

In this you have to go for compounding