If your spouse's employer withheld Virginia taxes, yet you are both residents of California for tax purposes, she will have to file a Virginia nonresident return showing that she had no Virginia taxable income. This will cause her withholding to be refunded.
You should also ask the Virginia employer to stop her withholding since she won't owe any Virginia tax. She can ask if her employer will do withholding for California, but they probably won't. So you two should look at your joint California tax bill and decide if she needs to do some estimated taxes to California through the year.
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