There is a long-standing question that gets asked every now and then about whether people should re-use a course or start a new course every time they get a different group of students.
When you copy a course into a new one, none of the comments from the first course come with the videos -- you start over fresh. The video itself is not duplicated, so it cuts down on storage requirements.
If you embed the same video multiple times within a course, the comments remain. Uploading the video again and then embedding the copy into a new piece of content (assignment, discussion, page, etc) is one way to remove the comments within a single course. Duplicating videos is not an effective use of video storage, which your institution pays for. If it is for a graded assignment, then you get extra material in your gradebook as well.
If your institution has chosen to reuse courses with different groups of students, then you may be able be able to get them to write some custom JavaScript that would hide empty comments.
I opt to create new courses each term. I have found a lot of reasons why it's better to do this and very few as to why you should reuse a course with a different bunch of students. Your example is just another case of why I like separate courses -- things just work better. I am term-based, though, and some with open/continual enrollment may see it differently.
You didn't go into why you are trying to get a different group to comment on the same video, so it is hard to do anything other than present options -- realizing that they may not actually be viable solutions.
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