'L' as in 'ls -a Desktop' and see if any of the files are shown there.
Do you remember if you turned on iCloud Drive for Desktop & Documents folders when you upgraded to Sierra? You can check in Settings-->iCloud-->iCloud Drive-->Options and see if 'Desktop & Documents Folders' is checked or not. If it is checked, check your iCloud account via webbrowser and click on iCloud Drive and see if your files are there and download them back again.
Also, make sure you are on the right Spaces desktop by pressing the mission control key (F3) and see if there are multiple desktops there and check each one.