Not sure what is going on but it seems steam sync related before I re-enabled it today.
If you think you've lost your game data suddenly check this path:
C:\Program Files (x86)\Steam\userdata\0\268650\ac\WinMyDocuments\From The Depths\Player Profiles

I am unsure why this happened, but I have contacted Steam.
Sorry for any inconvenience if this has happened to you.