You could unzip the 1.9 backup and remove the course files, rezip and restore that. Then you'll have a course with no files.
Otherwise, you can restore the course and then create a new course with no Legacy Course Files area and then import from the restored course to the new one. Then go and delete the large course that you don't need.
Not a very elegant solution, but that's what I did since I didn't know which files were being used and which ones were not. Some teachers were using courses to store files or they would not delete files no longer being used so this cleaned up all of that.