The vanilla playthrough will be removed in the next update, as it serves very little purpose, is not the main focus of the mod, and has caused plenty of trouble for us and for players.
Dark/er Light was a nice gimmick, but it's not worth the trouble of maintaining the vanilla game, nor people's confusion about having to replay or reset the game.
With that, the vanilla related achievements will also be removed.
Sorry, especially to the completionists who earned the achievements, but it is ultimately for the best.