After looking at my previous post I realized that it may be somewhat confusing for somebody not familiar with SH4 game files.
Among the many files and folders associated with SH4 there is a "Campaign" folder. This contains the data for the game's campaign and to the best of my knowledge the data in this folder never changes. Unless you install a mod that changes the campaign - then the data is only changed as the mod is installed. This is the data that would have to be changed between missions to create a dynamic campaign. My mod currently has nothing to do with this folder.
Another folder is the "SavedGames" folder. This folder contains the data that is saved when you save a game. My mod uses the data in this folder (it ignores non campaign saves). When I mentioned that I was creating new campaign files I may have been somewhat misleading. I'm actually creating new campaign saved game files like the ones in this folder.
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