What happens to the files that were formerly stored in the course files?
Good news is that the files are restored and that they are available in the site Server Files/Recent Files area of your file upload dialog box. I was able to move/rename and re-deploy said files without any issues.
What’s curious is that a few files which were associated with a Lesson module (which did not convert) were not included in the backup file restored at my test Moodle 2.0 site. It’s not apparent why, but a quick zip of your course files and upload them to the new course file structure at 2.0 should help to mitigate any other files lost. Here’s a quick video I made to highlight where you can find the files post conversion and restore.