It's always advisable to save in a different save slot every time, rather than to continually overwrite one solitary save slot. That way, if you encounter a game glitch, or a problem such as the one you're currently having, you can go back to an earlier, separate save.
Most games have unlimited save slots. Those that don't at least usually have a decent number of slots, so that the player can advance a decent way into the game before needing to overwrite an early slot.
When you go to your game load screen, do you only see one save file there? Or are there multiple ones to choose from?
"Bleat, Watson -- unmitigated bleat!" ~ Sherlock Holmes