If you select a non-empty directory and delete it, it will take a huge amount of time because Cyberduck will list it recursively to delete file contents in each subdirectory first. This is very inefficient for large directories and can take hours to delete!
There is a trick on FTP servers to delete non-empty directories that should be used.
Here is a link: http://stackoverflow.com/questions/10749517/ftp-delete-non-empty-directory
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