No, my files aren't gone, they just don't show up in the folders when you open them from outside the game or do a search. It's kind of bizarre. I've tried saving a couple of my missions to other folders outside the x86 folder and they still don't show up, even though with the mission editor they show up whole and hale. The funny thing is that it is just happening to my custom missions- the default .miz files included with the game all show up when I open the mission folder from windows.