You can file a North Carolina resident tax return and report all your active duty pay. For Virginia, because you changed residency, you can use Form 763-S to request a refund of the tax withholding and this will let them know your official switch date. Be sure to complete the questionnaire on the back of the form, and attach the documents requested, including your W-2(s).
(The Form 763-S is not in TurboTax, you can use the link to get it from the Virginia Department of Revenue and mail it in.)
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