There is no provision in the FA which disqualifies the employment of any handicapped person. However, you are correct in pointing out that a deaf and mute person may face more risks working in a factory from a safety standpoint. As a safety precaution, you can prohibit such a person from being near machines or machinery in motion.
You can certainly employ such a person and provide appropriate training. The individual has been employed with you to date, and you are satisfied with her performance, hence the question of confirming her services and ensuring her entitlement to PF, etc.
Please confirm her services and provide her with all statutory entitlements. She is eligible for all entitlements, so please do not prevent her from employment or her due entitlements. May God bless you and your company for the noble work of providing employment to such individuals.