I wouldn't think that you would have to start over from scratch, but if you are using CD/download software, you can delete the state and re-add it if you don't mind re-entering your Indiana data again.
However, I did note in my test that something I did after entering the quarterly income and credit allocations caused me to no longer have an underpayment penalty, and then when I went back, I couldn't see the screens for the allocations.
I did not bother to pursue this, since I figured that you would want to know how you got into the allocation screens...but just be aware of TurboTax's tendency to do dynamic screen sequences, which means that sometimes it's hard to get back to where you were.
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