Helium (carbon) won't recognize backup files
It's because the files within the com.koushikdutta.backup/files are deleted whenever

You uninstall Helium Backup, or
The phone has been factory reset

If those files are missing, Helium Backup will fail to recognize any of your backups, even if they exist and is easily restorable.
Requiring those files to exist in order to restore backups is honestly quite a retarded system.