With regard to this question, what I consider relevant comments by another user keep disappearing by unilateral moderator action - one of mine too (probably by the time anyone checks this, more than one), but mine are not the ones I am as concerned about. The other comments contained at least tangentially relevant links; blog posts and such where others had dealt with the question asked, and shared their point of view. It leaves a bad taste in my mouth, in particular on a site that I hoped would be interested in impartial analysis.
I wasn't a moderator involved - so I can't directly respond to motivations, but I can address some side issues.
Was this "unilateral moderator action"?
Well, in a way, all comment deletions are performed by one moderator - there is no voting involved, so it could be described that way. However, there was a system-generated flag warning all the moderators that the comments had got out of hand. Further, Sklivvz raised a flag on the question himself - rather than risk an appearance of a conflict of interest - requesting that another moderator clean the comments up.
So, I would argue that, no, it wasn't unilateral, AND that Sklivvz isn't an appropriate target.
@Larian did the honours - he hadn't been involved personally in the conversation - cleaning up side-conversations including comments posted by three other mods (Sklivvz and @KonradRudolph AND me!)
Could some of the comments have been saved? (Well obviously my pearl of wisdom should have been :-) ) Maybe; I'll leave that to Larian to defend. But Stack Exchange Inc's attitude to comments is pretty clear [a citation would help my argument!]: comments are second-class citizens.
I note there is now a chat room for discussion of the question.
The other comments contained at least tangentially relevant links
It's policy across all stackexchange sites to not have too many comments.
Too many comments can detract/distract from the questions and answers.
If a link were relevent then perhaps it should be in an answer, not in a comment.
As a (non-moderator) user I occasionally flag comments which (In My Opinion) are excessive or unwarranted in one way or another. A moderator will usually agree with my flag and delete what I flagged.
Although Sklivvze is a moderator he is also a user. As a user he is allowed to do anything other users do (including flagging comments for other moderators to act on).
This site has strict rules for answers: answers must be on-topic (must directly answer the specific question), must be referenced, etc. Answers which don't meet these criteria are deleted. Deleting these answers contributes to making this a high-quality site.
People sometimes post lower-quality answers as comments instead of as an answer: any such comments too ought to be deleted.
The best type of comment (i.e. what comments are meant to be for) are comments which suggest how to improve the question. Any other type of comment may be deleted. Even this type of comment can be deleted, after it has been used to improve the question.
This is a generic answer because I didn't read the deleted comments which you talked about. However, "tangentially relevant links; blog posts and such where others had dealt with the question asked, and shared their point of view" sounds quite off-topic for this site. The only content on this site is meant to be (basically) peer-reviewed evidence, not crowd-sourced opinion -- see How do I know that the information posted in this site is reliable?