Error Reading Config
Try removing the config file $ rm ~/.shallow-backup and running the program again. Config files from below version 2.0 are incompatible with the config files used after.
Missing Files After Changing Backup Path
Don't worry! They'll all be in the git repo, which was moved to the new path. The only exception will be any files that were not under git version control.
Try to cd into the backup directory and run $ git log. Then you can grab the last commit hash and checkout that revision. Your files will be there.