Save Files Messed Up ( Long Story )

[Bealla Donna]

So I started a new story to see the way diffferent choices affect the game with save file 2 yesterday. It saved fine and I was about halfway through the first episode and waited till it autosaved and quit. Today, the next day, I started the game only to discover save 2 is now "empty" and the only file that's been played apparently was my first playthrough which was about 2 weeks ago. So what happened?!? I almost cried because I hate losing progress in a game,espically losing over 2 hours of gaming. And the cutscenes are unskippable so I refuse to play again and have to sit through it all over again.
I clicked on the save and it showed me the "continue your story or start new story" screen. I clicked continue, It told me to adjust the brightness until the logo is barely visible, I did and it took me to the episode menu where I saw "continue episode 1". Erm...how? I thought it didn't exist. That it was erased from existence. I pressed continue and it took me right back to where I left off.
Ovbivously I'm glad it wasn't actually gone but it just irks me how It gave me that upset and that anger.
My first save is fine, has the date I last played and everything, choices are saved. But the second still swears it's empty and the choices won't load up. I know because I just finished it. Kept saying I was offline when my internet is fine and won't load my choices. Also had a weird bug where my mouse disappered and I couldn't respond to Riddler's Riddles questions. He was asking questions but the models were frozen, like Riddler is laying on the floor and batman is setting up his tech plan.
The only other problem I had similar to this was from TWD Season 1. That was really bad. I wanted the refund the game and get it removed from my libary so fast, even though I got it for free. The saves were f*cked all the way up.
So any helpful tips and/ or advice would be much appriecated.

Update: I copied save 2 into save 3 and It seems everything went back to normal. Well not completly. Still won't show me my choices and reletionships. Say's that i need to " complete a episode to unlock it" when I have. -_-
That also happened in TWD. Weird. Please tweak your save file system,Telltale. This is getting annoying.