First, the HSA contribution that is with code W on your W-2 and any other employer contribution that was not part of the code W amount will appear on the screen "Here's the income that California handles differently" early in the CA interview. This amount appears (unless you change it in the CA interview) on form CA (540NR) on line 1h, column C.
If you made any contributions directly to the HSA custodian (not through your employer), this amount appears on the same form, line 13, column A.
All three of these amounts will end up on the 540NR line 16 to be added back to CA taxable income.
If the W-2 with the code W amount are all CA source wages, then we don't need to adjust the code W amount - it will be added back to CA income as it should be .
"I do not see anywhere that my *direct/individual* contribution to HSA was added back to CA income. " - Take a look at form CA (540NR), line 1h, column C, and see if your direct HSA contribution is there (it should be).
"The reason I ask is because, as a partial resident throughout the year, though I made the direct contribution while living in CA, it was not actually all sourced through CA income because I pulled the direct contribution from my prior savings account. " I don't believe that you will be able to split such hairs. I imagine that CA's attitude will be: "you were in CA when you made the contribution on that given date, so CA will add it ALL back to CA income". The state is not going to parse where the money came from, only that the contribution was made on such and such a date.
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