My experience is that it can make a difference deleting the SH4 saves root folder and letting SH4 recreate it on the next startup. I have made many small changes trying to get it how I would like it and even loading from an autosave from port doesn't always guarantee the changes will be implemented or worse, it may make a mess of some other aspect of the similation. When I delete the save folder I always get the changes in the game. Sometimes I tweaked too much but you do get them.
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