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You are correct that if your W2 has an empty Box 1 and has Box 12 Code J (third party sick pay), then it is not necessary for you to submit this W2 with your return.  Third party sick pay (Code J) is not taxable.  Your employer was required to generate the W2, but it is not necessary for you to file it.  And, if you try to submit a W2 with a $0.00 in Box 1, the IRS will reject your e-file.

If the W2 is still showing on your return, then you should return to the Wages and Income section and remove this W2 from your return if it is still present.  You can use the search to get there -
  • Log into your account and click Take Me to My Return (you must click this before searching or you won't get the jump to link below)
  • Click the search icon in the top right corner (looks like a magnifying glass)
  • Search  for “W2” in the search box
  • Click the “jump to W2” link.
  • This will bring you to the appropriate place to delete the W2s

Now, I am not quite sure what you mean by "when listed it told us we had to E-file."  It should be the opposite - you won't be able to e-file with this W2 listed.  So, if the above doesn't help your issue, can you please comment back with further clarification about what you mean with the above statement.