I usually keep the save files from the game folder when I need to delete stuff to make space on my HDD but a lot of these games save to a secondary location so it should reference that (but I keep mine in case i need to move the folder into the new game folder)
Submit and...Control are the two sides of the nyx storyline. It refers to how you interact with her. it's possible that you get an error because you've never gotten a scene from that side of the storyline but i can't be certain there