Three years ago I wrote a manuscript and submitted it to a well-known journal in my field. After a few months, I received the reviews, which were extremely positive, but suggested minor improvements. I made the suggested changes, and the article was accepted. I signed the publication agreement and the article was made available in the "advance publication" section of the journal, with a DOI. The editor informed me that the article was "in the queue" for the print version. I was pleased and moved on to the next project.
Now, almost two and a half years later, I have received an email from the same editor. They write that "once we began editing your manuscript, we noticed a concern". They then list a number of things that they want changed. A few of these concerns are semi-reasonable, although I already addressed them with citations that point the reader to more detailed discussions in the literature. I could add some additional text to the article, however, if that is desired.
Most of the specific issues that the editor notes, however, are irrelevant to my article, and indeed have very little to do with my text. The editor desires, in essence, that I completely rewrite the text, redo all of the tables, and change all of the figures so that all of the results can be interpreted according to a very specific theoretical framework. The editor uses vague and imprecise terminology when making these demands, leading me to believe that they are not especially familiar with this specific framework. The editor's own publications contain nothing about this theoretical framework.
The theoretical framework is familiar to me. It is that of my former doctoral advisor. I disagreed with my doctoral advisor about this theory, as well as some other things, and after I completed my degree, got a job, and had some of my own publications, we no longer have contact. I am fairly certain that my formal doctoral advisor saw the advance publication and wrote a negative letter about my article to the journal's editor. My former doctoral advisor may be unhappy and irritated that I do not cite their work, or perhaps bears a grudge against me and wishes to harm my career. Additional information: Many years ago, my doctoral advisor was the editor of this journal.
I have no concrete evidence for this, but I am fairly certain this is what happened. I would like my article to be published, but I do not want to make the suggested changes, which, in my view, are ridiculous. I do not believe in this theoretical framework. A complete rewrite of the text would also require a massive amount of time. It has been three years since I wrote this article, and I am working on other topics now.
It also strikes me as extremely unusual, and quite unfair, to demand of an author that they make major changes to something that was accepted years ago. I am not sure what to do. Should I attempt to negotiate with the editor? Reach out to the editorial board of the journal? Should I contact the publisher of the journal? Are there any guidelines about this?