In 2.x, there are no longer "course files". Files that are associated with some activity or resource should come across when you restore, but files that were just in the 1.9.x course files area and not linked to anything will not.
Have a look here - http://docs.moodle.org/20/en/Course_files.
If users need access to 1.9.x course files, you might look at putting them into a repository, or users could upload needed files into their private files area.