My concern is that California is not going to smoothly process the nonresident return as filed and refund all of the California withholding. A California nonresident return showing zero California income, when the W-2 shows significant California income, will almost certainly result in a letter from the FTB saying that the California income was not reported correctly on the tax return. That will delay the refund and require correspondence with the FTB to try to convince them that the W-2 is wrong. Without any evidence other than the taxpayer's say-so, it will be hard to make that case. A letter from the employer saying that the California wages on the W-2 are a mistake would certainly help, if the employer is willing to provide such a letter.
