Use scatterbl.py from the scatter repo. See instructions here.
This script takes a folder with all basic level files in it, and sends them back to their correct location in Subject_Files
$: python scatterbl.py folder_with_all_bl_files path_to_subject_files [--audio] [--video]
The --audio and --video flags tells the script whether this folder has all audio files in it, or all video files. This determines where they'll end up in Subject_Files. You have to choose either/or. Can't have both.