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Yes, you can delete the state tax return without having an impact to your federal return. The federal information will re-transfer once you begin the state again.
However, it may mess up the information on the other state. If you are claiming a credit for the taxes paid to the state you are deleting on the return of the state you are keeping, that credit will go away when you delete the state's return.
For example, you messed up the return of State A and want to delete it. You are a resident of State B and that return is just fine. You are receiving a credit in your resident State B for the taxes you paid to State A. Once you delete State A, the credit on your State B return will also go away and you will see your State B taxes rise if you delete State A. In this case, you may also have to delete State B and start that one over after re-entering state A.
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