TurboTax pulls withholding from the Federal section, so it will override a direct entry on line 31a unless you override. An override makes you ineligible for e-filing and voids the TurboTax 100% Accurate Calculation Guarantee.
If your paper W-2 shows Kentucky withholding, add the KY income and withholding (and local tax, if applicable) as a new line on your W-2 in Boxes 15-20. This will transfer over.
Since the paper and electronic copies differ, double-check with your employer first to confirm that your KY withholding is correct.
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