The process of the IRS is a bit more complicated than that.
When you e-file your federal return, the IRS performs a quick check on certain things (like are there simple arithmetic errors?), and if nothing is found, your return is "accepted".
In the next few weeks, then IRS performs other checks, and if it finds a problem, the IRS sends you a letter. Then over the next year or so, the IRS does more check and if it finds a problem, they send you a letter, typically changing your return and asking you if you will accept the change.
On the whole, the IRS is mandated by Congress to get your refund to you as quickly as possible, and then the IRS goes looking for problems and errors.
Does that answer your first question?
As for HSA reporting on your California return, the contributions to the HSA should be handled automatically by TurboTax, as I noted before. However, you should have seen questions in the interview about your earnings - TurboTax cannot answer these for you automatically. Instead you must contact the HSA custodian and ask what your earnings (ordinary income and capital gains) were.
The representative on the phone will often have no idea what you are talking about because the HSA is tax-free in 48 or 50 states. So when you call, you may have to speak to a supervisor to find out any information.
Of course, since the HSA is just like any other investment account in California, it won't say "HSA" on the California return - you will just have to remember the numbers you put in and find them where the other investment earnings are.
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