Yes, you can E-File, but you should combine the two W-2's first.
Simply include the information in box 12 of the second W-2 with the posting of your original W-2.
- From time to time an employer will need additional room for extra information on the W-2.
- This may be why you received the additional W-2.
- When retuning to the original W-2
- Log back into Wages & Income
- Select Job (W-2) [Add/Edit]
- Select the W-2 using the down arrow
- Click [Edit] on the bottom of the screen
- Continue to the input screen
- Under Box 12a - 12b
- Click [+ Add another box 12 item]
- Continue the interview to the end.
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