I think the save game does disappear but you could ask someone else to confirm. When I booted up the game after patching, I didn't find my previous save file. Wasn't much of a problem for me since I wasn't playing this game due to the performance and textures.
When you think about why this game performs in such a slow way as opposed to many modern games with greater visuals and on-screen enemies, animations etc, there really is no answer.
This game is too CPU dependant maybe, since my processor is weak although other games run at max settings with my 8800GT 512mb graphics card and 2GB RAM. I'm talking about games with much higher quality of visuals and animations. Being a huge fan of Jedi Knight: Jedi Outcast and other Star Wars games, I wish the PC version was good.