Hello! When you load up a game data, it remembers where you are in the game. Now since we update the game often, sometimes we edit the scenario files. When this happens, the save position won't be where it's expected to be. This is why we don't recommend loading game data from a different or older version of the game. Does this answer your question? Other than that it's supposed to function as is. We can look into this just to be sure that the game data is saved and loaded properly.
Now there's something about the special scenes. I think I forgot about their data, so this means that when you save in the middle of a special scene, it might not remember the choices you made and you'll end up somewhere else in the special scene than expected. I'll definitely have to look into that one.