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The only marks that can go in the e-file are the ones the IRS can process. I'm pretty sure the IRS doesn't recognize any sort of superseding return indicator in the e-file specs. Do you have a link that says otherwise?
The IRS e-file system can file superseding business returns, but can NOT file superseding 1040s.
So you either need to e-file an amended 1040 or file the superseding 1040 by mail.
Page 24 of Publication 4164:
The superseding return designation is available for Forms 1041, 1120, 1120-F, 1120-S and 1065. The superseding return designation is not available for Forms 990, 990-EZ, 990-PF, 1040, 1120-POL and 2290. The amended return box must be checked for any subsequent Forms 990, 990-EZ, 990-PF or 1120-POL returns to be accepted.
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