Thanks for all the advice
Sometimes I have just left the computer on with the game paused, but I'd like to avoid this as I run SH3 on a laptop that is a few years old now and I worry that it'll get too hot and melt if I don't let it have some rest!
I did try just saving in the end, I made a few just in case any became corrupt. It seemed to work out on reload without any noticable problems.
Although I did try saving underwater just to see what would happen and that resulted in an immediate CTD when I reloaded, so don't do that

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