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I'm a MS student working on publishing my first manuscript. I wrote the draft, had it reviewed by my advisor (a co-author), then sent it out to my other co-authors for feedback.

Two of them (out of 4) strongly suggested removing a specific section in my draft, because they thought the results of the analysis are not meaningful. This was a section that I worked on, with some supervision from my advisor, and although the co-authors hadn't contributed to this section, I'm certain they fully understand what I did. I told this to my advisor, but he disagreed, and said that section is very valuable.

I don't really care if we keep it or remove it - I think it has some value, but not that much, and we can still get the paper out without that section. But I'm unsure how to reconcile the different opinions between my advisor and my co-authors. Should I follow my advisor's opinion and tell the co-authors we cannot remove this section? How should I reconcile the disagreement between my advisor and my co-authors?

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Note: I am assuming when you say "advisor and co-authors", you mean something like "advisor and external co-authors", and that the full list of authors is you, you advisor, and your external co-authors. If your advisor is not an author on the paper, then that is a different situation, as noted by Arno.

This is a fairly common type of disagreement among co-authors. In my opinion, the main thing here is to have a transparent discussion with everyone where everyone agrees on a way forward -- even though inevitably someone won't get what they want, everyone wants the paper to move forward so unless this is a really extreme case, there will be a reasonable compromise people an agree on. (And, if it is an extreme case, I would argue that it's not your responsibility to handle it, as a masters student).

I think where you want to get to is an open communication between your co-authors and your advisor where they agree to a plan of action. As a masters student, it's not really your responsibility to resolve the conflict on your own. But, you can gently push people in the direction of that outcome.

I would suggest telling your advisor about the arguments of your co-authors, and ask if your advisor would be willing to arrange a meeting (that could be virtual or in person depending on what makes the most sense, but ideally not email) with your co-authors to discuss this section. Hopefully, you advisor will agree and take on the responsibility to run the meeting. Alternatively, they may say that the meeting is a good idea but they want you to run this meeting. If you run it, let each person voice their opinion, and propose a compromise solution. This meeting can be stressful, but go in with some idea of what a reasonable compromise will be, and keep in mind that these disagreements are common and that even if people have strong feelings now, most likely in 6 months everyone will have forgotten the details and will be happy that the paper was published. My experience is that 95% of things that people say they feel strongly about when they are writing comments alone in their room, are actually things they are willing to compromise on when having an in-person meaning. In the remaining 5% of cases where there really is some serious disagreement, it's more productive to have an argument in person instead of by email.

If your advisor says that this meeting is unnecessary and doesn't support it, I would consider that unfortunate since it probably won't go over well with your co-authors, but in this case you can ask your advisor to send an email to your co-authors with their argument to keep the section and with you cc-ed. Then, proceed with what your advisor wants. If you get emails from your co-authors, forward them to your advisor, or respond with them CC-ed.

I'm basing this advice on the idea that (a) all things considered, it's easier as a master student to go along with your advisor and let them take the blame for scientific disagreements, and (b) you don't have a strong feeling about this section. If you did have a strong feeling and disagreed with your advisor, you could also consider trying to win your advisor over to your side.

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    @Andrew Yes he is a co-author, I meant "other" co-authors (other than my advisors) and edited the question for clarity. Thank you for your recommendations! I wasn't sure how much my advisor wanted me to be in charge of (especially since I'm considering on continuing on a PhD in his lab after I get my master's, and was worried if I would leave a bad impression on him by handling this inappropriately or not taking enough responsibility as a first author). Nevertheless, I will work on arranging an all-person meeting, thank you!
    – Jen
    Commented Oct 20, 2021 at 20:13
  • @Jen To be clear, he might ask you to take charge of this meeting, so I'm not saying that you won't be in charge per se. But I think it is responsible to propose a solution and get his feedback, and probably preferable to emailing your other co-authors directly agreeing to something your advisor doesn't want.
    – Andrew
    Commented Oct 20, 2021 at 20:23
  • @Andrew I'm happy to propose solutions, although I'm hoping ultimately they can reach an agreement, since I don't have a strong opinion either way. I'm thinking about cutting down that section or adding a paragraph explaining why that section may still be useful and hopefully the co-authors agree, otherwise Arno's suggestions below may also work for my advisor.
    – Jen
    Commented Oct 20, 2021 at 20:30
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(Note: This answer was posted when the question did not yet specify that the supervisor was a coauthor, too.)

Is your supervisor also a coauthor of this paper? If yes, then following Andrew's suggestion to facilate a direct exchange between your supervisor and the other coauthors is spot-on.

If your supervisor is not a coauthor for the paper, then their opinion on what should go in there is ultimately irrelevant. It was reasonable to mention to your coauthors that your supervisor really liked this section, but if the coauthors remain unconvinced (and you don't have other arguments you wish to present to them), the matter is settled and the section will not be included in this paper.

The section can always go in your thesis, and if you and your supervisor wish to do so, you could consider writing a second paper incorporating it.

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    Yes he is! I just edited the question for clarity. I also like the idea of putting the section just in my thesis or in a second paper if we can't get to agree on something. Thank you for your comments!
    – Jen
    Commented Oct 20, 2021 at 20:15

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