Yes, they will still take the scheduled payment. Some states have a telephone number to call where you can cancel a scheduled payment, but you'd have to search your own state's tax website to find that number...they are not always easily findable/accessible.
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That assumes you really set up a state payment when you e-filed. Not all states allow it to be done at the time of filing....if it was, it would show on your State "Electronic Filing Instructions" sheet that you were encouraged to save and/or printed just at the time you e-filed. It would look like the following:
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____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*