The first thing I would check is whether the second W2 you received is a "Corrected" W2. If it is a "Corrected" W2, you will have to file an amended return.
If you look at the top of the W2 and you see a box marked "Corrected" and it is checked, or if the W2 is marked "W-2c, Corrected Wage and Tax Statement" then you will need to file an amended return.
If it is not a corrected W2, I would contact your employer and ask them for an explanation.
If the W2 is legit and you need to add it to your tax return, you will need to file an amended return.
You will need to wait until the IRS has accepted your original return before filing the amendment. If you are to receive a refund, wait until you receive it before filing the amended return. If you owed the IRS money, then wait for your payment to clear.
For TurboTax Online, simply login to your account and select “Amend a return that was filed and accepted.” If you used our CD/download product, sign back into your return and select “Amend a filed return.
You can find out more about amending a return here
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