Unfortunately, with how the system works, it needs to overwrite the save in the current save slot every night. When you sleep, the game updates the inn (guests in and guests out) and saves it. If the VN systems didn’t save as well, it would cause the two systems to desync whenever you loaded a game that was a past day.
I’ll put a text notification to let players know it will save on overnights.
The best way to preserve a manual save is to make sure you save into another save slot to be sure your previous save slot stays untouched.