What a surprise!
This is getting ridiculous now. Last year I was happily playing TWD until episode 5 where my saves decided to disappear. Now I finally build up the desire to restart the game. I played 73 minutes of first episode and go away for 2 hours. I come back and what a . surprise. They have disappeared again!
As soon as I started to load up the game and noticed the resolution had reset I knew what was coming. How hard is it to have a game were the saves don't disappear. I've been gaming for years (probably too much) and never have I lost saves which weren't my own doing (losing backups/accidents).
I just bought the season pass for Wolf Among Us assuming they would have fixed the save issue, I now regret doing so. I wonder if I'll ever get to play episode 5 - I really do not have the desire to repeat that start again and most likely suffer another magical save disappearance. Though I'm sure I'll get the same copy & paste response and nothing will ever get done to try and solve the problem. It's one thing to allow a widespread bug like this to get into release, it is another to leave it for over a year and do nothing about it all the while ignoring the people who have it.
Support tool: http://www.sendspace.com/file/6wo599
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It's sad to see this happening, and I wish i could do anything about it, but I am just a volunteer trying to help, not a TTG employee.
I can tell you at least, that TWAU has an entirely new savegame system, which is intended to be more robust.
It looks like there's no way of restoring your latest playthrough, since the game crashed and replaced the prefs.prop in the savegame folder. Sadly I can't identify the cause of the crash though.
In most cases I have seen it's possible to restore the savegames, but crashes are bad in that sense.
If you are very lucky, you can use the "restore previous version" feature (right click, "properties", "restore previous version") on the prefs.prop in the savegame folder ( %USERPROFILE%\Documents\Telltale Games\The Walking Dead ) and make an earlier savegame accessible again.
Make sure you disable steam cloud for The Walking Dead before you do that (and leave it disabled indefinitely).
Either way, you should do some things to minimize the risk of having the savegame problem again.
First you need to delete the prefs.prop files from each of these foldes:
C:\Program Files (x86)\Steam\steamapps\common\The Walking Dead
C:\Program Files (x86)\Steam\steamapps\common\The Walking Dead\Pack
C:\Program Files (x86)\Steam\steamapps\common\The Walking Dead\Pack\default
If you were not able to restore a previous savegame, also delete the entire savegame folder ( %USERPROFILE%\Documents\Telltale Games\The Walking Dead ) before you start a new game the next time.
If you make a backup copy of the savegame folder every now and then, you increase your chance of success.
I know this is not a great way of playing, but it's all I can suggest given the circumstances.