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Are you looking at the refund meter or the actual tax form? If you are looking at the refund meter (the calculation at the top of your screen), then the refund meter during the amendment process only shows the differences from changes you made from your original return. Your original refund will still be paid to you. So, if your original refund was $1000 and now after changes it says you owe $100, that means you have to send back $100 from the original $1000 refund, not that your entire refund has been lost and now you owe $100.
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