I recently asked a question on meta "Will my account be closed like that of [insert-here-the-user-who-shall-not-be-named] if I stop participating on Physics SE?". It was being downvoted so I added a comment below it "why downvotes?". This was followed by a (peaceful) discussion between me and Manishearth. During this discussion Manishearth told me that my question broke no rules and so (on this basis) i refused to change the title of my question. However then one of the moderators (Shog9; who, as I just knew, is also a stack exchange employee) came and deleted all the comments also changed the title and main body of my question. I further added a comment that the changed title was not what i asked, to which he only replied after two days.
I want to know the rules moderators/stack employees follow in deleting comments in an ongoing discussion. Manishearth in his answer below says that there are no rules which, if true, is ridiculous because you can never question the action of a moderator even if s/he deletes some comment which is very useful to the discussion.