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We recently had a c.s. theory / networks paper accepted at a special issue after addressing a major revision. After we got the letter of acceptance, author proofs, signed the copyright release, etc., we got a letter saying

the paper was inadvertently marked as "Accepted" which was not the decision of the guest editors of the special issue. Apologies for the confusion.

They then ask us to strengthen our revisions to the same reports we responded to before:

Please understand that although we believe that you made a considerable effort in revising your manuscript, we think that reviewers' comments 5, 8, 9, and 11 require further attention.

But they misinterpret what the referees want in those points. One example is that the referee originally asks

Why not use testbed experiment to evaluate it?

(we have given reasons in our paper why testbed experiments are not necessary) but the editor writes

the reviewers ask to perform testbed experiments

They close with

If the paper is successfully revised and the reviews are positive, then it could be accepted and appear in a later addendum to the special issue.

In short, the editors claim to have accidentally pressed "accept" and then forgotten about our paper for 2 months while it went through the editorial and publishing process, and that we have not met the reviewer's demands, which the editor has clearly misinterpreted.

How do we proceed in a way that ensures our fair treatment and, ultimately, the publication of our paper at this journal?

  • 3
    A fun thing to do would be asking the journal to officially sign back the copyright to you. – Federico Poloni Nov 29 '16 at 19:58
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Unfortunately, these things do happen sometimes, and there's not much you can do about it. If the journal does not want to publish your paper yet, there's not much you can do to get it to publish your paper without carrying out the revisions that they request. At least they caught their mistake before it was actually published, unlike in this case at PLOS ONE, so you don't have a retraction on your record.

I would suggest you treat this just as any other request for revision: improve the paper and hope that the next revision is sufficient for publication.

  • I should emphasise that this new letter is not one of rejection. The paper is still "conditionally accepted", but they are setting the bar higher (by misinterpreting the original referee reports. edit: I have edited the question to clarify this. – Alejandro Erickson Oct 24 '15 at 18:59
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    @AlejandroErickson I've adjusted my answer accordingly --- basically the advice is the same: just ignore the mistake and move forward as though you got their intended statement originally. – jakebeal Oct 24 '15 at 19:16
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No one here can tell you what will insure the publication of your article beyond satisfactorily making the changes that the reviewer wants.

On the other hand, I have had at least one successful case writing a strongly worded, polite, and well-reasoned rebuttal letter to the editor explaining why the reviewer is wrong. You might be able to convince the editor that the article is fine as is so that it can be published without additional changes. This route probably has lower odds of success since you have to convince the editor that they were wrong and that their hand-picked reviewer is wrong, but if what the reviewer wants is impossible or nonsensical, you might have to try this approach.

You might try writing the letter and not sending it. Get a couple of close colleagues who are not co-authors to read the paper, the reviewer report, and the letter, and tell you how they feel. You don't have to send it. If you can't convince a friend, maybe you shouldn't try to convince the editor.

Edited to add: This is a strategy that you should only undertake with the help and complete assent of your current co-authors. When I did it, my PhD supervisor and I were the only authors. He agreed, strongly, that the editor was wrong to agree with the reviewer, and we worked on a nice rebuttal letter that was convincing. We sent it under our joint names, but it would have appeared to have come from me more since I was first author and we listed my name first in the letter.

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