It has been brought to our attention that there currently is an issue in the game, where you could seemingly lose your progress if hardware was changed.
We have found the issue and will work a fix into next Tuesdays patch.
In the meantime, the good News is, that Community Member SLEMPHI wrote a guide on how to get your savegames back.
Check out http://steamcommunity.com/app/423620/discussions/0/451852225142210267/ to use it.