In order to recover a not listed and hidden folder, do as follows:

  1. Launch Secret Folder.
  2. In the main window of the app, click on the "+" button while pressing the Option-key.
  3. In the dialog that opens you will be able to see either a visible or an invisible items, locate and select the files or folders that you want to make visible (please note that items contained in a invisible folder are themselves invisible, so if a file is located in an invisible folder, to make the file visible you just need to make visible the folder that contains that file).
  4. Make visible the items you chose using the Visible/Invisible switch button in the main window of the app.

Please note that Secret Folder uses the standard functionality of OS X to make files and folders invisible. The files and folders that are hidden, remain in the same place that they were when they were visible, and they move when you move the folders that contain them and are also copied and deleted along with the folders that contain them.