As TRON.dll found out, this problem with saves going missing is a Games for Windows Live issue. It's not specific to Evolution. It happens in all GfWL games.
What's happening is that GfWL treats offline saves and online saves as being different. If you sign into your account online and play the game, you must ALWAYS keep signing in. Or if you stay offline when you start the game, you must ALWAYS stay offline.
If you switch mid-game between playing offline and playing online, GfWL will erase the one type of save to make room for the other.
So to save yourself the headache, just always sign in and play while you're online. That way, if you were playing offline but then decide you want to jump into a multiplayer game, you won't lose your progress because you forgot about not going online.
Either type of saved game can be easily backed up, so that if you ever end up losing your progress, you can copy back the save file and you are good to go again.
And yes, this idea to treat offline and online saves differently is an extremely stupid decision.
As for bugs, I only encountered one. Sometimes Anon will freeze up during combat, and won't animate any more. So you have to die in order to continue. But this same bug occurs across all versions of the game.
I applied a change in the configuration file to skip the branding intro so it can jump right into the start screen. I hope it doesn't happen to me.
Nah, that won't make it happen.