Affiliation in conflict-of-interest situations This is a follow-up question to What affiliation to put on an academic paper for alumni authors? Some time ago, I read a paper published in a journal owned by my employer which was very far-fetched. It espoused a very non-mainstream theory. It looked so far-fetched that I couldn't believe the journal would accept it, but I confirmed with the desk editor of that journal that it wasn't a mistake. I also saw the review - the reviewer agreed it was very speculative, but couldn't outright call it wrong, and so recommended acceptance.

I could think of reasons why the theory was wrong, so I wrote up a letter to the editor and submitted it to the journal. 

Question: what's my affiliation? From aeismail's answer to the above question, my affiliation is where I did the research work. That makes my affiliation the publisher (however I was not contracted to do research work, and I did this on my own time). However there's potential conflict-of-interest here since I'm submitting to my employer's journal. If I listed my employer as my affiliation, it might seem that I've circumvented the normal peer review process. In practice the peer review process happened as normal, and I was not involved in it at all, but this would not be apparent to anyone not an employee of the publisher.

I got out of this dilemma by listing the university that granted my most recent degree. They maintain a university email address for life, so I used that. Nobody has complained, but I'd like to know if this was the right affiliation.
I disagree pretty strenuously with what you have done.

First of all, being an alumnus is not an "affiliation".  If you weren't a student or employee of the university at the time you did the work, it's not your affiliation and should not be listed as such.  You're welcome to list your alumni email address if you like, but that's your contact information, not your affiliation.

I would say your affiliation is your employer, the publisher.  Or, if you feel strongly that the work was done "on your own time", then you may omit any affiliation.

However, independently of any of this, you had a duty to disclose your employment by the publisher, as a potential conflict of interest.  Conflicts of interest may exist regardless of your affiliation and must be disclosed.  You can certainly add additional information that you think may help the reader evaluate the issue (e.g. "I was not involved in the review").

I have to say I'm pretty concerned with the notion that you would "get out of this" by concealing the potential conflict.  That's exactly the wrong instinct, and contrary to every principle of academic ethics.  You address conflicts of interest by disclosing them.  The fact that "nobody has complained" isn't dispositive; it's not their job to find and disclose your conflicts for you.  What you've done can be grounds for retraction all by itself (see for instance https://retractionwatch.com/category/by-reason-for-retraction/failure-to-disclose-coi/), though if the omission seems to be accidental, a published correction can suffice.

If the letter hadn't yet been published, I would advise you to contact the editor and ask for a conflict-of-interest disclosure to be added ("the author is an employee of XXX but did not participate in the review of the cited paper").  Or if that is not possible, to withdraw the letter.

In this case, you say the letter was published long ago, so it's less clear what to do.  Probably the safest course of action would be to write to the editors, apologize, and ask that a correction be published.  I don't think it's necessary to correct the affiliation per se, but rather to correct the fact that your potential conflict was not disclosed.  It's possible they will decide that retraction is more appropriate, but that's their call.