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The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
Ignore any 1040V voucher that prints out and the new 1040. Those are what your return would have been if you had not needed to amend.
If you already paid the tax owed, then you will get a refund. The amended return assumes that all refunds were paid or all tax debts were settled before the amended return was prepared. In other words, if you originally owed $500, and you paid it, and the amended return shows you should really owe $400, you would get $100 of your payment back as a new refund.
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