When trying to delete a large directorystructure Cyberduck (Version 2.5.4 (1881)) uses information from it's cache, which leads to lots of 'file not found' dialogs which each block the process. Very annoying bug.
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But marking all directories in the cache as invalid and requesting a new file listing will make performance much slower. The cache should only be out of date if you removed some files through other means than with Cyberduck.