Sorry, in the interest of thoroughness, it's story time:
Yesterday when I booted up TWD on Steam to play 400 Days, the game warned me that it was going to generate story decisions for my skipped episodes. Instead of a game complete save, apparently it had me saved at the final checkpoint of Episode 5, right before you tell Clem to get the keys, the gun, or both from the (un)dead security guard. I went ahead and finished it again because there are some pretty important choices there at the end and I wanted to make sure they carried over to TWD2 (can't wait!).
Then I jumped straight into 400 Days and played through the first 3 stories before stopping. But today when I went back into the game, it gave me the exact same warning that it was going to generate story decisions for skipped episodes when I tried to load my save.
I went ahead and copied my save to be safe this time and loaded up Episode 5 again. After going through the warning that rewinding was going to erase my progress in future episodes, it put me back into Episode 5 at an even earlier checkpoint. This time it was immediately after getting off the street and waking up in the jewelry store, after seeing Clem's parents.
So I fiddled around with that for a minute then exited back to the main menu. When I went back to load my game for some reason the copied save had disappeared and the primary save file had changed to one where Episode 5 was completed. Hoping that it had magically fixed itself I hopped into 400 Days (no warning about generating story decisions this time) but my 400 Days progress had been lost.
I exited the game again and rebooted it. Unfortunately, the singular Episode 5 completed save had reverted to the old messed up save and its copy. Even worse, this time whenever I would try to load up Episode 5 in either of those saves, the game would go to a black screen and stay there. It wasn't frozen, I still had full control over the pointer, but it would stay black and never actually load the episode.
So rinse, repeat, I exited the game and rebooted it, this time going into 400 Days and opting to generate story decisions. It had definitely lost my 400 Days progress and loaded back at the beginning. I played a minute into Vince's episode before returning to the main menu. Again, my two saves had become one.
Checking on the decisions it had generated for me in Episode 5, it attributed me as having told Clem to leave Lee behind. I don't know if that's what normally happens but it is accurate to the decision I made when I beat it months ago then beat it again yesterday. I jumped back into the singular save in 400 Days and it loaded me back into Vince's episode without a hitch.
So one more for the road, I exited and rebooted the game a final time. The singular save had yet again reverted to the dual saves with Episode 5 still incomplete, but thankfully it was now properly loading into the episode again right where it left me, immediately after entering the jewelry store.
I went ahead and included the dxdiag data file. It would be great if there's a fix but I'm starting to think that maybe my only recourse is to play through the end of Episode 5 again, then churn out all of 400 Days in a single sitting. Anyways, thanks for your time. Let me know if you have any questions for me.