I'm sorry I can't be a real help for you, but this type of thing has happened to me only when the game has crashed while saving. That has corrupted the file the way you mentioned, at which point there was no way to fix them... Has your game crashed while saving? I recommend to never use the option to 'Save and Exit' from the menu, but to Save separately and then shutting down the game. The game has crashed two times when I've tried to Save & Exit, corrupting the file, so I stopped doing that.
To avoid losing sims when the files get corrupted, you could try going back to a previous save. The game creates a backup file automatically, so if something goes wrong, you can try and go back to your previous save. Instructions are here: http://www.carls-sims-3-guide.com/forum/index.php/topic,6.0.html
If you want to be extra careful, you can create multiple save files by yourself. Every now and then, use 'Save as...' to create another file of the same game. Then, if the worst thing happens (both the game and the backup get corrupted - I've had this happen), you won't lose everything.
I'm sorry I can't suggest anything to help fix your game crashing and corrupting files, I really don't know what the reason could be. I hope these tips were still helpful.