The behavior of the automated transfer is correct. In point 3, The program does not delete folders. If "Delete files after transfer" option is selected, only files are deleted during automated transfer process . Hence the original folder structure remains unchanged. In point 4: If we have some files within the folder then that folder will be created. For example if we have a folder "level 1" and a sub folder within it say "level 2" and now if "level 2" has some files within it then this folder structure will be created at your local drive, since it is required for copying the file from the ftp server.