I imagine they are still working on this one but here is the workflow:
1. Upload an old 1.9 backup into a new 2.x site for conversion.
2. The conversion fails because of such-and-such plugin not available.
3. Left with a "Course restore in progress" course in the 2.x site.
4. Re-backup the 1.9 course without activities using the broken plug-in.
5. Re-convert and select "overwrite existing course" to wipe out the "course restore in progress" broken course.
6. New course appears. File repository for legacy files is not available.
So the short version is:
If I overwrite a broken course restore with a legacy backup file, the legacy file repository is turned off when I need it to move things to the new method of managing files.