Because you are a part year CA resident CA will do a weird math thing to figure out what your tax due is. But they will still add that HSA back in in order to calculate the total income "as if you were a California resident". After the system has done that then it will calculate the taxable portion due to California and that is where the HSA entry that you make will make a difference.
The FTB doesn't have an article on this HSA difference but here is a piece of legislature that is aiming to change the law and it has a lot of good informatio... about the current law towards the middle of the bill.
@notarobot1
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