Thanks a lot! This really helped me to pin point the bug, it was route specific. The error was in the final quest of Abbadon, in which it should had changed a story variable but it didnt.
If you played i.e. Alba first and then abbadon, you wont have that error, or if you didn't did the art's route. I am sure a lot of people have this bug but just thought that was all the content of the game.
It is fixed now, although sadly I dont think there is a way to "fix" the save, although I will add in the next release maybe a bug fix that could re-start the questlines for those who have found this bug, although I hope that number is low