Okay, it may not be this, but I'm going to chuck it out as a possibility as it happened to me. I re-installed Windows 10 and accidentally selected the option where it saves stuff to OneDrive by default. So rather than looking in C:\Users\username\Documents\The Witcher 3\gamesaves it was looking in C:\Users\username\OneDrive\Documents
(actually I don't think it happened with this game, think it was Civ5 I was trying to play after a fresh install and couldn't work out why my game saves were missing even though I'd copied them over, but could be the same.)