If she has destroyed your property, then that is an enumerated offense, which would entitled you to an order of protection. You should seek the aid of counsel to help you with this matter.
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Although one must wonder how in view of what you wrote, "life is going good...," the only way to keep her out of the house via an order of protection is by bringing a family offense petition if she engages in one of the enumerated penal offenses, or the equivalent charge in local criminal court, or by seeking a divorce and asking for exclusive occupancy to keep the peace at home. You should discuss this with an attorney as well as other possibilities.
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You can file for an Order of Protection seeking a stay away or you can file for divorce seeking exclusive use and occupancy based upon her destruction of property.
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It's all done in one shot, though it's a bit complicated. You will have to file an action for divorce, and a Petition for an Order to Show Cause and Temporary Restraining Order giving you exclusive possession of the your house or apartment. You really need a lawyer for this, it's kind of involved.