I would not understand when you say "Family Court" isn't including one of the children. Family Court doesn't file petitions - either ACS filed a petition or you did. Either way, the petition can be amended to include the other child. As such, you should consult a NYC Child Abuse lawyer for a full assessment of the situation.
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Speak with a family law attorney and bring in a copy of all the paperwork.
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Just because "no one contacted the cops" then doesn't mean you can't report it now. After talking to a lawyer about the family court matter, call the police or prosecuting attorneys office(s) in the place(s) where each of the incidents occurred.
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