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