Just for the information of the community (because we've spent the last couple of days thrashing through this issue and want to save you the same effort):
When you restore
- a v1.9 course backup archive
- to an EXISTING v2.1 course
- choosing "delete the contents of this course" (don't know if this is significant or not)
The Legacy course files area is NOT created
When you restore
- a v1.9 course backup archive to v2.1
- selecting "Restore as a NEW course"
The Legacy course files area IS created.