Desktop icon turned invisible

From time to time, one or more icons on my desktop become invisible. I finally got smart and used Everything to search for them, and saw they were still in the Desktop directory. I then made a shortcut and put that on the desktop -- but how can I restore the original and prevent this happening again?

I think I've found the problem. I use Stardock Fences to corral sets of related files and programs. I had accidentally shoved one Fence too far so that part of it was beyond the display--the missing icons were there.