OK... interesting... I don't see anything that should cause this but it's rather hard to investigate.
Could you try and either retrace your most recent actions that you think caused this... OR, if you have some kind of cloud share like Google Drive or Onedrive, could you upload your most recent save file so we can take a look at it?
Just so you know, your save files in the actual game data folders are N+1 of how they appear in-game (save 1 is technically the autosave slot, so slot 1 is save 2, slot 2 is save 3 etc.)