The issue of the "emptying save files" happened to me several times after the first. But, at this point I'd been regularly backing up my drones so it wasn't as much of an issue. What I figured out though, is that this happens when the computer does a hard reset while the game is running. The fact that there was an update right after the first instance was probably just a coincidence. I also don't leave the game running when I'm not using it any more. So, I haven't had this happen to me in a long time and this issue may have all ready been fixed; I just don't feel like going through trouble of testing it.
On a side note, one time my save file was corrupted when the game crashed. But because of the information given to me in this thread, I was able to open it with 7zip (winwar wouldn't do it) and recover half my drones. Thanks.