When I create a new knowledge base version from an existing version, not all article level settings are copied over.
For example, if an article in my existing version has "Related Articles" linked in the article settings the copied version does not include those "Related Article" links. I am now forced to relink all "Related Articles" for each individual article in my new knowledge base version.
I have not checked to see other items that don't get copied over, but in general if I am going to copy something it should be an exact copy where possible.