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After you file
No. To amend you need you need to wait until the IRS is done processing your first return and you get the first refund. Have you entered the missing W2? If you did then take it out. You don’t enter it until you start the amended return. The amended 1040X won’t be ready until Feb 19 or later. Where does it show your return looks way lower? If your first return was $2,346 and with the missing W2 it should be only 139 then you have to pay back the difference of $2,207.
You will still get the refund from the first original return or still need to pay the first tax due. 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.
Then the amended 1040X return is only for the difference you get back or owe. I think the cover sheet shows what the original return WOULD have been if you did it right the first time. Ignore the new 1040 that might print out.
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.