Is it islamically appropriate now that the mother has completely left Islam and only causing harm and damage and is a danger even virtually now through emotional and mental means, is it appropriate to have the father stop contact with the mother due to the safety of his son? Because the son himself is scared of his mother and is now being emotionally unstable because of her.
All she does is cause problems and there’s many witnesses to this.
The mother also is not guiding the son to Islam at all.

Yes if the mother is posing harm or danger to them, he is justified in cutting ties with her. This would be permissible since he is obligated to protect himself and his son. If in the future she becomes stable and the threat is removed, he can have his son resume ties with her