1d42392 created the issue

Cannot copy empty folders to new location. For example, create folders and subfolders in dir X. Open another browser window. Select dirs, hold down Option and drag to new window. Icon indicates files being added but nothing is added. Copy the dirs, select Edit > Copy X files. Select target folder (in same or another window) and select Edit > Paste. Result: nothing pasted.

Open File Browser in cPanel in your favorite browser. Select empty dirs. Select Copy Files. Enter target path and click OK. Result, all empty dirs are copied to target location.

Refresh view in Cyberduck of folder in which empty subfolders were added. Folders that were added and can be seen in File Manager cannot be seen so that they can be populated files.

Quit and relaunch Cyberduck. View folder in which empty subfolders were added. Folders and subfolders can now be seen.