Is it considered bad practice or unethical to remove some references/citations between the initial paper submission and the final one? I submitted an 8-page conference paper, it got peer-reviewed, it got accepted, and now I have to submit the final 6-page version. In order to cut down on length, I'm thinking of removing some less important/relevant references that I included in the initial submission.
Are there any general "rules" against that? It's an IEEE paper btw.
You are of course entitled to add or remove parts of your paper to adhere to length and content guidelines of a conference or journal. If such changes lead to a change in the references being cited, then that is reasonable. Of course, it is also reasonable for the journal or conference to determine if the changes that you've made affect the overall quality of the paper. So it cuts both ways.
In general no major changes should be made to a paper after acceptance unless either requested by the editor or, if suggested by you, approved by the editor. There are of course trivial changes and there are major changes that can result from making removing materials in a paper. When a paper becomes accepted, it is considered ready for publication by the editor. If you then make changes to the paper (apart from correcting spelling or grammar) you need to communicate these to the editor and make a good case for why you need to make them and how you can ensure they do not alter the content and more importantly the basis for your conclusions. The reviewers have reviewed the paper with all the information included and in the worst case your paper may not have been accepted were not all of it there.
So making significant changes after acceptance is not to be toyed with and consulting the editor is necessary.
The problem in your case lies, as pointed out by dgraziotin, in that you need to shorten the paper after acceptance which is normally considered too late. On the other hand, if the editor asks you to do so, then I would assume the editor will see to it that the reduction does not significantly influence any vital parts of the logic and reasoning leading to your conclusions. In such a case you will need to follow instructions, the responsibility for accepting the paper with the final revisions still lie with the editor and you have not done anything unethical or wrong. I will, however, say that the order of matters seems jumbled within the organisation of the conference peer review system.
Every paper is written with one thing in mind: making a contribution to your field. If, by removing a citation you are impacting the quality of your contribution, then it needs to be left in.
Having said that, I think the section of your paper the reference is in could help you determine if it's making an impact on your contribution. If it's from the related works section, and you have plenty of related work, then no big deal - remove it. But ... if it's directly in support of your contribution, then removing it may have more impact on what your trying to accomplish, and you should find a way to keep it in.
A paper is not accepted until the editor says it is. Having a glowing referee's report is not the same as an acceptance; at best it is "provisional acceptance". In this case, the editor wants additional changes regarding length. If these changes can be made to the editor's satisfaction (which may include sending the revised version to referees again), only then the paper is accepted.
My advice is to do the best you can, and to address your changes in your cover letter. Honestly, how much space do your references really take up in an 8 page paper? Most likely you can make the cuts you need in the body.
