Should I submit a paper to a journal whose staff I am challenging? I would like to submit a paper to a particular journal. The problem is that I am critiquing the analysis of several individuals who work for the journal or are on their editorial board...and I'm providing evidence that proves their theories were incorrect. I'd like to know how to handle this, as my paper challenges their theories (and the motives behind their theories). Would this create a conflict of interest for the journal? And would my critique harm my chances of having my paper accepted for publication?
First, I do not think the term "conflict of interest" applies here, so I do not expect the editors will reject you paper just because their work is somehow related with your paper. Nevertheless, it can get quite tricky to get your paper accepted by this journal and it highly depends on the editor's ability to receive criticism, but even more on the quality of your publication! So to increase your chances, you should consider the following.


Never get personal: A paper is not a place for ranting about other people. Make sure that it is very clear from the paper that it is not the people you are challenging (as expressed in your question), but only their theories. Otherwise, this will surely result in a rejection, even if your work is otherwise groundbreaking.
State the positive aspects of the editor's work, too: This highly depends on the topic. For example, if the theory still applies to some areas, state this clearly. Even if you are not sure about this aspect, you can write something like "Our analysis has given a counterexample that shows that the statement by xy et al. is not as universal as assumed, but future work is required to find the conditions under which it is valid." And even if their theory is completely bogus in you opinion, take the editors point of view, for example with statements such as "The experiments conducted by xy et al. could lead to the conclusion that ..., but future experiments presented in this paper show that the results should interpreted differently.".
Stay calm in your wording: Keep your emotions low. Do not attack or challenge their theory. Even prove the theory wrong might be too strong. See the previous paragraph for better examples which are of course highly dependent on the topic.
Do not provide attack vectors: Every weak part or minor mistake gives a good opportunity to reject your paper, before even thinking about the validity of your arguments. Too many typos -> reject, weak related work section -> reject, unreadable fonts in the figures -> reject.
Explain your arguments very good: Do not expect the editors even understand what is wrong with their theory if you explain it to them. Unfortunately, it is a human tendency is to stay at the own belief, even if the arguments are strong enough to convince a neutral person (think about all the conspiracy theories).
Expect competition: Even if the editors are very open to publish a publication that contradicts their work and your paper is generally good enough to be published, you still compete against other good papers. If the journal usually publishes x papers per year and the editors think there are x submissions that advance science more than your publication does, they will take these x submissions. Do not expect a bonus here and keep in mind that even papers that do not challenge the editors usually have a hard time of getting accepted!


All in all, it is important to submit an excellent publication!