Is it unethical to change the affiliation of a published chapter from my PhD thesis after candidature?

Question

I completed my PhD research at the University, submitted my thesis draft for examination, and began working at a company co-founded by my PhD supervisor. Before completing my thesis examination, I submitted a portion of my thesis to a conference. Upon its acceptance, my supervisor, now my boss, advised me to list the company as the paper's affiliation, which I did. For more context, please refer to this previous question I posted several months ago:

Can I publish my thesis content with a new affiliation although the work was mostly done in the previous institution?

To provide an update: When discussing the final approval of my thesis with the dean of the university after getting my examination results, he noticed the changed affiliation in the published conference paper. He voiced his displeasure, stating that it was unethical, particularly since most of the research was conducted at the university. He even hinted that he could withhold my degree because of this change in affiliation. However, he mentioned that if I refrained from acknowledging the company in the thesis, he would grant approval. To avoid jeopardizing my degree, I complied with his request and received my degree. But this situation made me anxious about the possibility of not earning my degree.

This experience has prompted several questions. Upon reviewing the university's regulations, I discovered I possess full intellectual property rights to my thesis. Does this suggest that I can choose any affiliation I want for its chapters when publishing them?

1. Was it genuinely unethical to change the affiliation as my supervisor suggested, considering that the majority of the research happened at the university?

2. Does the dean possess the authority to withhold my degree based on the changed affiliation, especially when the university's regulations indicate that I have full intellectual property rights over my thesis? I was not sure whether he was just angry and bluffing or if he was serious.

3. In the future, if I encounter a similar situation, should I follow the directives of my boss or supervisor? I followed his instructions because I didn't think it was a big deal. Had I known the dean would react this way, I might not have complied. But what's done is done.

Answer 1

I think the fact that legally you own your thesis work is irrelevant. Regardless of whether or not you broke a rule, you pissed off the dean.

1. I'm not sure I'd call it unethical exactly, but it is incorrect and misleading. You completed the work during your time at the university. It is not really appropriate to list only your affiliation with this new company. In most fields, listing multiple affiliations is totally normal - this is probably what you should have done in the first place (correct me if I'm wrong, but I'm reading the situation as you removed your university affiliation and replaced it with the company). The dean feels what you did was wrong. I don't disagree - the university has invested time and resources into the project (directly and indirectly) and wants credit.
2. My gut says that yes, an upper level administrator would be able to cause you problems. I doubt even the dean of the university could unilaterally decide to not award a degree though (assuming you satisfied all requirements and haven't run afoul of some official rule). Obviously this would be dependant on many factors, including you universities specific policies. In any case, I don't think you were wrong to do as he instructed.
3. In the future, you should list your affiliations normally. If you are in situation where you have multiple affiliations, just list them all.

I don't think you handled the situation perfectly, but your dean's actions where not right either. Obviously as a student you are in a vulnerable position. He clearly leveraged that power differential to force you do what he wanted. It makes me wonder if he has some feud with your advisor and saw you as an easy target.