I am going to say cause nobody seems to dare say it.
This is an early access game. Saves are not guaranteed to carry on to next patches. It is suggested to begin a new play through until the release of 2.0, with the release of every major patch.
Yes it is possible to migrate save JSON files from one release to next. But this should be undertaken with extreme caution that it may corrupt your game.
I really wish Kal would put something on the main page about this.