When deleting the Save folder, just delete the whole thing, either from "C:\Users \UserName \Documents \SH4" on down, or data or cfg inside of that, and on down. You want to remove all files from in the Save folder after most major mod changes. The game will recreate the folder, even if you have used MultiSH4. What happens when you add mods, is they change the game's configuration. Since the game runs off of the data inside the mod folder, and the way JSGME and Windows work is to not overwrite existing files there, a lot of changes made by a mod are not transferred to the Save folder, which can introduce crashes. When the folder is deleted, the game will re-create the structure there, but will use the new data from the mod, and then you can eliminate that as a source of trouble - usually. The only problem with doing this, is that you do lose all progress in the game, and if you might want to continue where you were later, it is all gone. If you want to save the Save folder for later use, you can copy it elsewhere first, but just remember that if you do try to reuse it later, that the game mod condition must exactly match what you had, else you end up with trouble again.
