I've used the same 'Save' formula since day one of SHIII. I save 'in port' before each mission and I overwrite the previous 'in port' save each time. Then I rotate between two overwriting saves every five minutes within a mission.
So I have TDK1 (in port), TDK2, and TDK3 (in mission saves). I've been doing this since March 2005 and I've yet to have a problem with either game.