If she has a good reason to move, most judges will allow her to do so.
However, a threat to leave the jurisdiction before a law suit is filed is a reason to grant an Ex-Parte Emergency Custody Order to maintain the status quo until things can get sorted. If the separation agreement has been made part of a Court Order, then you should be able to file a motion to modify custody/visitation (your visitation will need to be changed if she moves across the country as the current schedule will no longer work) and could possibly get an injunction prohibiting her from moving until things get sorted.
See an attorney ASAP!
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You probably already have an answer to your question. You need to file a motion in the custody proceeding for an ex parte order to prevent your wife from removing the children from North Carolina prior to a hearing in your case. Relocation cases are always difficult, and it is unclear from the facts you have given whether there is a legitimate reason for her move. You need to request modification of the custody order and a transfer of primary custody to you based upon changed circumstances, i.e., your wife's decision to move.