Hello,
Sorry to hear you are having issues. Need few more details.

1. Have you tried restore saved backup? If you did not yet, please try this first, try those older one. Do know that Fences by default save daily back up up to 7 days.
2. Need to know, where is those files physically located? In your Desktop folder or in some other folder.
3. Was those Fences were Folder portals Fences or normal Fences? 

Thank you,
Basj,
Stardock Community Assistant.

Yes it could restore the location of the Fences if it moved to somewhere visually that make you can't get to them. But, it can not by itself add, remove or recover deleted files/shortcuts/folders from your system. Fences is just your desktop organizer not a file manager. It does work with file manager to delete something. What you can do is, check your desktop folder and see if those missing file stills appear in your actual desktop folder. If it does, Fences should be able to display it properly. 

If those missing files also missing from your desktop folder. Most probably something has delete it off or move somewhere else. Which from what I know is something Fences by itself can not do.

Thank you,

Basj,
Stardock Community Assistant

Perhaps you can try any of those files backup application.

Thank you,

Basj,
Stardock Community Assistant