As long as you can identify the amount of income that was sourced in California, you should be able to complete the California nonresident return. You will need to manually adjust the business income in the state return section. The federal section doesn't have the ability to earmark income by state.
Likewise, for your expenses you can either allocate based on the relative amount of California income or use your actual expenses (like travel) that were tied to the income from California. Reporting expenses would reduce the taxable CA Income.
We recommend that you complete your nonresident return first, then work on your resident return.
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