You may be able to avoid the issue you raise regarding your W-2s if the SDI you received is not taxable by the federal government. In this regard, the federal government doesn't tax short-term disability benefits in California, unless the SDI payments are a substitute for unemployment insurance. Were your SDI payments a substitute for unemployment insurance? If not, then your SDI would not be subject to tax on your federal return. Follow-up with additional information if necessary.
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