It's not caused by a corrupted savegame file. It's caused by a bug in the game that wasn't discovered until several weeks after VV3 was released. We believe that we have found the cause of the bug (a timing problem with the game's autosave function), and the fix will soon go into testing. It is unlikely to occur twice in the same game, but there is a way to prevent it from occurring until the fix is available: make a quick backup of your savegame files before launching the game. That way, you can put the game back the way it should be if something bad happens.

You can find the backup and recovery procedures for VV3 here.