At the time of purchasing wine shop you should have done due diligence. You should have cross checked whether license was in single name or joint names. If mother had died and left a will whether any probate was obtained. Whether in pursuance to will the mother name was deleted from license. You have mentioned that all agreements were provided to department. Without going through the agreements we cannot advise.

It appears that 3 months after transfer of license you have received letter from department that license cannot be in your name. It is your case that license has been transferred in your name by collector and all the fees have been paid by you. If license has been wrongly transferred in your name Govt can revoke the transfer after considering your reply and after granting you a personal hearing. If you are aggrieved you can challenge the decision of Govt in court.