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Children's Services will do whatever they think is best to protect the child. That being said, if he leaves his girlfriend and she doesn't have any more contact with the children, I don't know that they'd change custody to ex-wife. They would certainly try that if they felt like he was continuing to allow his child to live with a person who was potentially abusive. It doesn't matter if he was not charged, if they were to feel like he was allowing the child to remain in a potentially dangerous situation, they would definitely seek to remove the child to the other parent. They could ask him to take classes, even if he wasn't charged with anything, if they think he might be making some poor parenting choices.
There is nothing stopping them from trying. They do not have 'rights' per se, but they do have the duty to do their job. Their job is to protect the child. If they have any reason to believe that the child might not be safe, they will do what they think is necessary. It doesn't always seem fair, right, or make sense, but that is what they will do. His best option would be to present all actions he has taken to make sure his child is protected.
They should give him a plan to follow in order to see or get his child back. It would probably be in his best interest to hire a lawyer or consult his local legal aid office to see if they can help him. CPS will often do and go until they are ordered to stop by a Judge.