If you are seeing a refund this is likely a refund of the amount that you just paid in with your return. When you do an amendment, the refunds/amount due reset to $0. When you enter the additional information and see the numbers change, these numbers are correcting the numbers you paid in. For instance, if you paid in $1,000 and you are seeing a refund of $350, this means you still have a tax liability of $650 so if no corrections would have been necessary on the original return, you would have had a payment due of $650.
Using the same example, if you're seeing a refund of $1,350 then you would be receiving your original payment back plus an additional $350. If this is the case, you can attempt to contact your state treasury department by phone to have them stop your withdrawal, however, generally they will remove the money from your account and then issue you a refund for the over-payment.
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