Good afternoon Lisa,
If you file for emergency custody, the court is going to expect you to take custody of your daughter---not send her to live elsewhere.
If you do not take custody of her and CPS takes her from the father, they could place her back with you, or she might be placed in a foster situation until you get court approval to have her come back to you.
At present, he is the custodial parent, based on your agreement to that and based on the fact that she is living there with him---regardless which of you may be paying support to the other.
Even the non-custodial parent has custody rights
. The support order may have him paying you---but you allowed your daughter to go live with him. That means that CPS is not just going to hand her back to you. the court presumably will---which is why you need to petition the court immediately for custody.
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I wish you the best in 2013,