The calculations are on the tax return themselves. Since you are using desktop, use "Forms Mode" to look at the California return. The nonresident return will have a "Federal Amount" and a "California Amount". The Federal amount will include the HSA. The California amount will not. The prorate will be the California amount divided by the Federal (including the HSA). California tax is calculated on the full Federal amount, and then prorated using the formula I just described. The HSA is not directly taxed. However, when factored in to the Federal column to determine the imaginary tax, it can raise the tax a bit if you are in a higher CA tax bracket because of your income than the tax rate at which you were withheld in California. I just duplicated your situation to see for myself, and the tax did go up a little bit including or excluding the HSA amount. However, that is CA law. The HSA is factored in to determine your CA tax.
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