Yes, you should file a non-resident Virginia return for a refund.
If Virginia state tax was withheld and paid to the State of Virginia, and you have not been a resident of Virginia for at least two years prior to the sale of the stock, you are not obligated to pay Virginia state tax on that income and should file to have that tax refunded.
According to the state of Virginia:
“As such, in the interest of fairness, the compensation earned from the appreciation of stock acquired through ISOs will not be considered Virginia source income for nonresidents provided that the individuals were not residents of Virginia for at least two years prior to the sale of the stock.”
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