THE problem is that there are a few DESKTOP folders.
Windows is suppose to take them all and place them into the one under PROGRAMDATA folder. If the shortcuts aren't in there moving or renaming the shortcut will make it disappear.
Now, I figured this out and copied them to that desktop folder, then lately found an easier way to fix it but I can't remember.
So lacking stumbling across that solution, just find the folder they are in under ALL USERS or your profile folder and copy them to C:/ProgramData/Desktop/