Actions that are taken on folders that are set to recurse are ineffective using SFTP. For example, changing permissions or deleting folders take forever. This is because, looking at the logs, Cyberduck is doing this one file at a time. Here is the log for deleting a folder named "test" with four files inside ("foo", "bar", "baz", and "qux"):

OPENDIR
READDIR
READDIR
CLOSE
REMOVE
REMOVE
REMOVE
REMOVE
RMDIR
OPENDIR
READDIR
READDIR

And on the bottom of the window, the status shows it deleting every file individually.

SFTP seems unable to remove the directory and all its files (even when run from the command line), but what does often work is SSH'ing in to the server and then running:

rm -rf <directory>

Or, for permissions:

chmod -R <permission> <directory>

This doesn't always work (it is OS-dependent), but it should be presented to the user as an option.