Hello Allen,
I don't think UJF_FILE_SERVICE_CLEAN_LOGS was designed to delete folders but we can verify this.
In the meantime please ask the customer to delete the folders manually through UJFS. It may take a few minutes but it is a one time clean up. After the initial time they can just continue to maintain the folder structure so it won't be a problem.
Best Regards,
Leila Lappin