When you amend your return, you're starting out at zero. Anything you get back on your original return you'll get back. Anything you owe with your original return you'll owe.
The amended amount (whether you are getting an additional refund OR owe additional tax) is a separate transaction.
So in your case, you'll get the original refund check back first, then owe on your amended.
That's why it's important to wait till you get your original refund back before you amend. You have till April 17 to pay the amount due with your amended return.
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