There seems to be a bug where the game only recognizes save files in the first slot. I got around it by renaming my last save file, but it's a bit obnoxious to only have one save slot
This should be the case. Try backing up your save folder and re-download the game. Then place your save folder into the same place in the new release and check out the result. This way, Yorna should track all your save files, not just one.