The game kept crashing after I got to the Black Cove & tried to save, so I deleted all my old save games. Now when I start a new game then open conversations with npc's it shows dialog & quests that I haven't started. I am tempted to uninstall then reinstall the game, but I am concerned that I might lose access to the game. I've never been involved in an alpha level game. So I don't know what will happen if you uninstall it.
Yea, I've got the same bug when I started new game - the state of the gameworld from previous games is saved somewhere else besides saves. You can easily delete local content on Steam, the alpha will still be shown in your library of games and you can reinstall it again.