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My coauthors and I have submitted a paper to a fairly prestigious journal. We have received favorable reviews and were in the process of incorporating the reviewer's suggestions into the final revision.

Unfortunately, a few days ago a crank paper was published in the very same journal. The paper received a whole lot of publicity, and has severely damaged the journal's reputation. We no longer have confidence in it.

We plan to withdraw our paper and submit it to another, more reputable journal. However, we are not sure how to go about this, since the current version of the paper already contains acknowledgements pertaining to the anonymous reviewers (who have done stellar work) and their suggestions.

What's the appropriate way to acknowledge these reviewers in the new submission? Should we submit a new version of the paper to the new journal, leaving out the acknowledgements to avoid confusion? Should we leave them in and write a letter to the editor of the new journal explaining the circumstances? Something else altogether?

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You acknowledge the referees by writing "We thank anonymous reviewers for important and insightful comments on an earlier version of this manuscript."

This is no different whether your paper was previously rejected from another journal, you withdrew it from another journal, or whether the reviewers worked for the journal where your work is ultimately published.

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I would not rush to withdraw the paper. "A few days" does not seem to me time enough to know that the "prestigious journal"'s reputation will be "severely damaged".

Since the paper has not been finally accepted, it can't be published until you submit the revised version. Wait a while to see the dust settle. Talk to colleagues. Then decide whether to withdraw.

If you do withdraw and resubmit elsewhere you can acknowledge the contribution of reviewers of an early version of your paper.

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    I upvoted. I am showing my age here, but it used to take more than “a few days” for a “prestigious journal” to do the death spiral down the porcelain convenience.
    – Ed V
    Oct 27, 2022 at 0:45
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    @Z.A.K.My recommendation is in the last paragraph of my answer. But I do think you should wait.
    – Ethan Bolker
    Oct 27, 2022 at 0:54
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    It's a fairly prestigious journal in my specific field. Not a top journal in mathematics in general by any means. The Annals could obviously survive a case of publishing high-profile crankery. The journal in question won't. That said, I'm really not interested in discussing or debating the specific case, whether our judgment about the fate of the journal is right, or whether withdraw our paper is wise (and this is not a discussion forum anyway). Was merely interested in the proper procedure of acknowledging the previous anonymous reviewers.
    – Z. A. K.
    Oct 27, 2022 at 8:01
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    It is utopian to expect that a journal never makes a mistake. A single cranky paper is likely to be dealt with in time: retraction, correction, etc.
    – Buffy
    Oct 27, 2022 at 13:36
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    Not if the author is also the journal's editor. Related math.SE question: mathoverflow.net/questions/433278/…
    – Avery
    Oct 27, 2022 at 17:53
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If the editor who handled the paper is an editor at multiple journals, you could ask if they would consider let you withdraw and submit it at their other journal in which case they would just use the same referee reports. It's not unusual for referee reports to be transferred like this. You could also ask for them to send the referee info to another editor at another journal, but that's a little riskier because they could be offended.

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    That would raise a conflict of interest for the editor unless the journals have the same "corporate" parent. And ethical editor would refuse any such request.
    – Buffy
    Oct 27, 2022 at 13:33

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