Secret Folder uses the standard functionality of the Mac to make files and folders invisible. In Unix based systems, like macOS, files and folders whose name starts with a period are invisible. The files and folders that are hidden, remain in the same place they were in 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.
Also, all the files and folders contained in a folder made invisible are themselves invisible. For example if a file is located in an invisible folder, to make the file visible you need first to make visible the folder that contains the file.
The items you see in the Secret Folder window are just aliases representing the original items present in your disk. It is possible, in some circumstances, that aliases loose the link to the original items. If you don't see an item you previously added, please refer to this solution: How to recover a not listed and hidden folder.
Note: programmers and experienced users could gain access to a folder or a file made invisible. Also please be warned that there are some applications that let you open files contained in a folder made invisible.
Related Links:
How to recover a not listed and hidden folder
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Spotlight shows hidden folders
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