When you download a file and overwrite a file that is a symbolic link on the local machine Cyberduck does something very weird. It should open a file pointer on the symbolic link and the filesystem will handle writing the contents of the file to the location that is referred to by the symbolic link.
echo "Hello world" > file.txt
ln -s file.txt link.txt
See that file.txt has now become a symbolic link to 'Hello world?' - it's not even a file anymore.
Thanks for a great FTP client!
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This seems to work here without any issues. What is not supported are the old style 'Alias' created in the Finder.app. These will get transferred as zero-sized files. Please reopen with more details (the output of ls -al before and after the transfers) if you can reproduce this issue.