Don’t start with SELECT CHAPTER or you aren’t gonna be able to save your game at all.
Next, when you exit and come back to your game again, press CONTINUE.
DO NOT click on SELECT CHAPTER or all the progress you’ve made will be lost!
If you see Bendy icon flashing rapidly on your screen for a minute or two instead of disappearing into the abyss then that’s the reason why you start so far behind from the last save.
Simply restart the game once you see it (NOTE: restart from Steam, not Main Menu).
You may lose some progress, depending on how quickly you noticed the glitch, but at least you’ll be able to save again.