Oh I guess there has been a misunderstanding because I found Vrook on Dantooine, the Mercenaries were there in the cave with him and then I told the Mercenaries they can ship him to Nar Shaddaa. Then after I had made the deal with the Mercenary leader and attacked Khoonda , then Vrook was there and I killed him.
I am not sure why Atton is standing alone there in Dantooine because the beginning of the save file was right after the discussion with Kreia. Maybe the reason why Atton is there is that when I exited Ebon Hawk after landing at Dantooine, you get to select party members normally, so I picked Kreia and Atton. After the cutscene of the Exile entering the Rebuilt Enclave begins, all other party members disappear somewhere and when you wake up after betrayed by Kreia, you are alone, as in the beginning of the save. So I don't know why Atton didn't physically return to Ebon Hawk for example, because that's where he is when he tells you in a cutscene how Handmaiden took Kreia and what not.
I am not using any other mods than the ones mentioned in the first post. I will try to summarize here the order in which I did things:
1) After Telos my first planet was Nar Shaddaa, found and killed the Jedi Master as intended.
2) From Nar Shaddaa, I went to Dantooine, found Vrook and killed him after a tough fight. Despite that, the "Lost in the Shadows"-quest entry didn't disappear from the quest log.
3) I went to Korriban, did all the stuff there and got the clue about Vash going to M4-78.
4) I completed the first part of Dxun and Onderon by asking Dhagon Ghent to arrange the meeting with Kavarr and then betrayed Kavarr by backing Vaklu.
5) While Onderon was on cooldown, I went and did M4-78. I found Vash inside , and killed her and got her silver lightsabre.
6) Went back to Onderon, helped Vaklu to assault the palace where Kavarr was waiting for me. The fight went really fast, I am not sure if I skipped the cutscene where Kreia was supposed to comment to me about his force form. But he died anyway and after that I let Vaklu troopers to kill Queen Talia.
7) After Onderon, I flew to Dantooine, took Kreia and Atton to my party, and went to Rebuilt Enclave.
So yes I am not sure what went wrong. :s I thought that "Lost in the Shadows" would have completed itself/disappeared when Vrook died but it didn't. I guess there have been no other weird things related to the main storyline. Thank you for fixing the save, I will try it out and see if it works as intended.