Was playing on a save of 14 hours when suddenly I was unable to save and both of my save files were simply gone. I restarted the game to see if that would fix it but the files were still missing. I started a new game and it saved just fine. The missing saves are nowhere on my machine. Not my recycle, not my desktop, not my documents, nothing.
Viewing post in Caliross, The Shapeshifter's Legacy comments
I have heard about this happening very rarely. The most common cause I know of is if you try to save when the game's folder is located in a restricted folder on the PC (like "windows" or "program files"), and another one can be if the folder got set to "read only" somehow. More rarely, if a script got added/changed and you load an old save, sometimes things can go wrong too (but I don't think I changed any scripts in recent months).
Basically, it's a freak accident and more often than not it's not an issue with the game itself, so sadly I can't really "fix" it.