When you restore a course into an existing course, choosing to add content to it or choosing to add content deleting existing content will not allow for legacy files to restore.
To duplicate issue:
Restore 1.9 course that contains files into an existing course, choosing to delete contents and then restore on a 2.x site.
View course after restore and Legacy files are removed from course
When you restore a 1.9 course into a NEW course on a 2.x site, Legacy files are included.