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After you file
Probably visit a local tax pro to get it straightened out and filed properly. (and NOT one of those seasonal storefront operations)
I don't think your "advice" from the agent you talked to is correct (Unless you were a college student with a CA home address, but in NC just for college). The address that is on the W-2 is immaterial. What is important is which state you were a resident of at the time you earned the income. (but that's my non-professional opinion)
(Assuming you were not a CA resident, and not just in NC for college) …..What you "should" have done when you filed your 2015 taxes, was to have prepared and filed part-year tax returns for both NC and CA. Both of those state Part-year tax returns would have started with BOTH W-2 forms entered as full-year income, but you would have allocated just the NC W-2 as NC-resident income, and just the CA W-2 as CA-resident income during their preparation. IF you didn't do that, then yeah..CA might complain and come back at you, for not at least starting with both W-2 forms to indicate total yearly income.
You can't amend your 2015 state tax filings to correct things, unless you already have 2015 Desktop TTX installed on your home computer, with both states too, since the 2015 tax software and states and updates are no longer available. (And I can't know if you really did it right anyhow...but from your explanation so far, doesn't sound like you prepared&filed the state forms properly).