Journal unsatisfied with revisions after acceptance, author proofs and copyright 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?
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.