There are a few files that can ~
sometimes~ (emphasis on "sometimes") be kept from the Save folder, but it is easier and best to just delete the whole structure. The game itself runs off of the Save folder data, and any leftovers can and will cause trouble, including those select few files at times. The RichSavedGames folders are binary files that should especially be deleted, since they hold data from the previous saves and configuration. After you delete the folder, the structure is rebuilt by the game, and you do have to set your configuration choices for gameplay, screen size, etc., but even keeping those few files can be problematic if there are changes in those basic files from a mod's config. I know of several mods do in fact change those files. It is best to be indiscriminate and just delete the whole Save structure when changing major mods, or as mentioned, using MultiSH4 to set a new folder structure.
