I finished KOTET it was an awesome storyline and was really sad that it wasn't longer... That's why I decided to do the aftermath quests, I saw that you could marry Lana in nathema conspiracy at the end of the traitor story arc. When [spoiler ALERT] you finish the flashpoints before nathema conspiracy and Theron betrays you, There's no more quests after that, so like many people who've had the same problem as me, you think that the traitor story arc is finished. So you check your ship's mission terminal to see what's next, and the only quest that's there is Jedi Under Siege. Sure, it gives you a warning that it will skip the traitor arc, but remember, you think that it's finished... So you play Jedi Under Siege. At that point many people would think that Nathema Conspiracy is AFTER Jedi under Siege. But you will soon realize that it was after the traitor arc (for me, it god knows where, I never seen the option to have Nathema Conspiracy as a main quest). And you will realize that you skipped PERMANENTLY [bIG SPOILER ALERT] Nathema Conspiracy, The marriage proposal with Lana/Theron, That the gravestone is destroyed etc... A big, Important part of the story... And you can't go back. I'm really disappointed, I wished that I would've completed these mission but now It's irreversible... Hope that some day the developers will fix that for the future new players...

Dude, that is completely on you. Not on the developers, one quick google search would've been enough to settle your doubts about the timeline here and it's not like the game doesn't help. I'm pretty sure you get the rest of the traitor's arc quests automatically anyway, and Ossus has multiple warnings letting you know it'll auto-complete everything before it.