Why are empty folders/directories being created in the source?
A common mistake is to create a Smart Sync, or synchronization, profile instead of a backup (or Fast Backup) profile. This article describes the differences between backup and synchronization. If your profile is a Smart Sync profile then it will synchronize folders as well as files, so if a folder exists in the destination then it will also be created in the source. With a backup profile no folders or files are copied from the destination to the source.