You will still get the first original full refund (and keep it) or need to pay the first tax due. You should not amend or change your return until you get the refund from the original return or your payment has cleared.
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.
The amended return is only for the difference you get back. Like if you paid $500 tax due on the original return and with the changes you only would have owed $300 then you only get a $200 refund on the 1040X. But if the amended return would have changed your original tax due into a refund then you would get the amount you paid back plus the new refund.
Go by the actual 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.
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.
