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After you file
See this TurboTax help article as to what "accepted" means:
What does Accepted mean? (intuit.com)
An "accepted" return can still be subjected to further scrutiny by the taxing authority.
It is not at all uncommon for a taxing agency to find errors or omissions on a tax return, even though the return initially appears to be correct when it leaves the taxpayer's hands. What TurboTax guarantees is that its calculations will be correct. But the program of course cannot guarantee that all of a user's entries will be correct.
A 4963 notice from California means that after a review the taxing authority made a change to your tax return which resulted in your having a balance due. The letter should contain instructions as to what steps you should take if you disagree with their findings.