You will still get the first refund or need to pay the original tax due. Then the amended return is only for the difference you get back or owe. In fact you should not even amend until the first return has fully processed and you get the first refund or your tax due payment has cleared. And make sure the original refund or tax paid shows up on the amended return. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund. If you paid on your original return it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
