This is a bit of a mess. The problem is that your home state will give you a credit for taxes you pay to CA, so that means you need to file a new original CA return, an amended home state return (unless you live in a state with no income tax), but do not need an amended federal return.
First, let's make sure you actually owe CA tax. If your permanent home is in another state, you only need to file a CA return if you have CA-source income. CA source income is generally 3 things.
1. If you are a W-2 worker, CA income is income from any days you physically work in CA, even if you are only there temporarily.
2. If you are a schedule C taxpayer (single member LLC or sole proprietor), income is CA-sourced if your clients are located in CA, even if you never set foot in the state.
3. Certain other income, like capital gains from selling property located in CA, or having rental income from CA property. However, simply owning shares in companies that are located in CA is not CA-source income, nor are payments from a CA state pension, as long as you live outside the state.
CA might have sent a notice because they got a whiff of your involvement in the state, but that does not prove it is CA income.
If you agree you have CA income, the normal process is to prepare your federal return first, your CA non-resident return second, and your home state last. CA only taxes CA-source income, and you have to manually allocate your income, Turbotax can't do it for you. (For example, if you worked 2 weeks in CA on a W-2 employee job, then 2/52nd of your income, or 3.84%, is CA sourced.) You prepare the home state last, so that the tax credits for out of state taxes compute properly.
So to start with,
1. are you sure you have CA source income?
2. does your home state have an income tax?
3. do you have your data already in turbotax, or was your tax return filed some other way, so you are starting from scratch?
