If you have evidence she leaves the 9yo home alone, you should report your concerns to the Court & see if the Judge will order a CPS/ACS investigation. I also agree there's a chance the evidence of your knowledge of her leaving your then 1-year-old alone may backfire, to the degree that if she was neglectful in doing so, then you may be found to have acquiesced to her conduct (unless you legitimately believe she stopped after you confronted her). In any event, I'd highly suggest that you schedule a follow-up consultation with a NYC Child Custody attorney.
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Deciding on what kind of evidence to present is a judgment call that a skilled attorney can make after he/she has as much information as possible regarding the case.
This is a difficult question to answer, however, if you had knowledge of the issue, and didn't mention it for two years, a Judge may not find that information overly persuasive as to your assertion that she is an, "unfit," mother. Further it may call your decision making into question. You should definitely speak to an attorney about this matter.
You and your attorney must decide this in view of the other evidence in your case. It might be better to just focus on present "wrongdoing" which affects the child. You are equally blameworthy on the earlier incidents.
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