Chamilo LCMS Connect » Courses

A new version should never undo the publication of an existing version, otherwise a user would not create a new version but simply change the existing object.
This is the main reason of the introduction of versions: to make it possible to work on new versions of an object without any effect in existing publications (also but not only in the courses application).
An example: it should be possible for version1 of an object published in course xyz2010 to coexist with version2 published in course xyz2011.

I have a question in return: what is the functionality/use of versions in the present implementation? What is the precise relationship with publications?

The use is that you can save several versions of a publication and you can easily revert to an earlier version, this is done via the repository. So the difference with simply editing a publication is that the previous publication version is saved.
The functionality you describe (having several indepedent publications of a same object) is achieved by Publish -> Browse -> select object(s). This way you can create as many publications as you want of an object, in different courses.

If I understand well: a new version of an object saves the previous version, but not the publication?
As far as usability is concerned this is simply unacceptable.