Two years ago I read a paper in which the "Methods" section did not report enough information to reproduce the analysis presented by the authors.
I contacted the first author in order to have more information and he provided me the code he used to analyse the dataset presented in that paper.
I found out that in the code there was a conceptual mistake in the way some algorithms were used. However, I did not have a solution for the mistake. So, I just ignored the fact and started working on a different problem.
One year later, while working on the new problem, I found a solution that could permit to avoid the conceptual mistake that I found in the above-said paper. As in the meanwhile I stumbled across to another paper doing the same methodological mistake, I thought to write a letter to the journal in which the first paper was published to underline the problem in those two papers and propose a solution. The paper analyses a simple dataset in order to show the differences between the results obtained with the old method and with my new method. I also (of course) point to the fact that the data presented in the two papers should be re-analyzed, as a data analysis containing that mistake can produce misleading results.
The peer-review process went smooth, with constructive comments of the reviewers. At the end of this process the Editor informed me that they also requested a signed review by the first author of the paper published in his journal. So, the same person who originally provided me his code.
The recommendation that he gives on my paper is of major revision. His comments are (in principle) constructive but he requires me to cancel from the paper the reference to his paper because: i) the re-analysis of his dataset with my method (re-analysis that he did not share) does not show significant differences; and ii) the criticism of his results is not justified as the Methods section in his paper does not contain sufficient details to infer the error. Do you think that these request are justified?
During a private conversation with me he also made clear that it is his interest to make sure that his original paper "would not be destroyed" and that he does not consider to publish a re-analysis of his data. This is particularly nonsensical because the results affected by the error are just a rather small part of the results presented in his paper and could only be found out by inspecting the code.
Given this context, I think that his requests are quite unfair. It is clear that he is just trying to preserve his publication record. It also makes clear that all his positive comments in the review are just an attempt of bargaining a positive recommendation for the publication of my paper in exchange of erasing the reference to the error in his paper.
Therefore, my conundrum is if I should just give in to his requests for an easy publication (nice thing during a PhD) or do not bend, argument against his comments and get a rejection recommendation. What would you do?