Unfortunately, the same thing just happened to me twice. I played up through Episode 4 and then went to play it one day and it started me all over at episode 1.
Then, thinking I must have hit a wrong button, I played all the way back through again and made it about halfway through episode 5. I went to finish the game today and it did it again...erased everything and back to level one upon hitting "play."
While I loved the game, unless this is fixed, I'll never play it again. I put in many hours because I wanted to play through using the choices I made. So when it got deleted, it just turned me off to the whole game. Really a bummer