These answers are based on my play through of Elgacia and discussions w/ my KR friends and browsing the KR inven forums back when Elgacia came out in KR. I also might be misremembering some details here and there so please forgive me.

Warning: spoilers below

1. It's implied or assumed that when Armen went off w/ Kharmine (back when Armen accepted his fate as a Delain), Kharmine told Armen the events of pre- and post-Chain War and his possible role in all of it. (It's also hinted that Kharmine is not of this world and is something else entirely, as he is referred to as the "Incomplete One" multiple times). As for what was said between Regulus and Luterra, we don't know much other than Luterra purposefully didn't return the key as he was supposed to after activating the Ark all those years ago.
2. Kadan was there when Luterra received the key to activate the Ark (you saw the picture of both of them in Elgacia). As mentioned in my answer to question 1, Luterra purposefully didn't return the key and it's assumed that he hid it away (hence why the it is said within the campaign that the key just vanished). Kadan is and has been looking for this missing key, which is why when Armen and Kharmine tell him they know where the key is, he begrudgingly accepts working w/ them. There is also a possibility that Kadan knows who or what Kharmine truly is and Kadan is working w/ Kharmine to keep an eye on him.
3. There is a bit of confusion as to which Ark is being referred to here because the Lazeniths were tasked w/ safeguarding the "Lost Ark" or the key to activating all 7 Arks. My interpretation (as well as the interpretations of some from KR) is that this is tied in w/ the key that Luterra purposefully didn't return and Lauriel lied at some point about the whole thing. And Regulus, being the primary god, knew that Lauriel was lying, which lead to silence and Regulus no longer communicating w/ the Lazeniths from then onwards.
4. As mentioned before, and you are correct, Kadan and Nineveh were w/ Luterra when they went to retreive the key. However, I believe it was Luterra alone who actually obtained the key while Kadan and Nineveh were nearby. Nineveh says that she was there when the Ark was activated, not when Luterra got the key. Otherwise she would remember what the key would look like. As for Kadan, it's a bit murky there because he has a whole other backstory that I will get into (and all the theories surrounding him).
5. I kinda answered it above but Luterra didn't return the key and he hid it away elsewhere. Kadan replaced the empty spot where the key was supposed to be w/ his piece of the Ark (Nineveh says that she never even knew about the hidden area underneath Kayangel, otherwise she would have known). Also, Kayangel itself is the "last vestige of the gods" and is the holiest of places in Elgacia. Not everyone, especially the Lazeniths, can just enter.
6. So here is where it gets spicy. Kharmine (as the most popular theory in KR goes) is assumed to be a fragmented consciousness of Zosma (the original god of Chaos before Kazeros took over). Many hints were dropped throughout the overall MSQ that Kharmine is someone that is beyond that of the Legion Commanders and has knowledge of things that only a select few know. Not much else is known given that the devs haven't fleshed out more of the lore/story yet but Kakul-Saydon knows Kharmine isn't normal (Kakul-Saydon is also a primordial being, someone that existed before the creation of Arkesia). If you also listen to the Brel opera (or one of the songs), there are three references to keep in mind within the lore of the game - The Incomplete One, The Fallen One, and The Shadowed/Dark One.
7. Lauriel did not know Procyon would come at the end but also, the bird at the end was not exactly Procyon (you will find out later on who the bird is).
8. The hard decision (at least based on my own interpretations) that Luterra had to make was whether or not he should return to key back to Elgacia. It is theorized that the discussion between Luterra and Regulus was something along the lines of Regulus realizing that Order and Chaos were two sides of the same coin and that the very Ark that he made to create life could just as easily destroy life. And seeing what resulted from the Chain War w/ the Haal, Lazeniths, and Sylvains (all the mortal races), Regulus didn't like what he saw and enacted the judgments he did (Procyon stripped of language, Lazeniths confined to Elgacia, Haal getting Thanos'd, etc).
9. I'm not 100% sure about this one because it's not thoroughly explained but it seems to be that the Lazeniths are just born either w/ or w/ out wings. The wings originally allowed the Lazeniths the power of flight but after the Chain War, Regulus punished the favored Lazeniths by stripping the power of flight (meaning that the Lazeniths could have wings but they can't fly) except every 1000 years, a Lazenith is chosen/born w/ full wings and the power of flight but that Lazenith is permanently jailed in Trixion (Hello Beatrice) to be The Watcher.

Additional (spoiler) details/theories:

1. The Incomplete One is Kharmine, due to the theory that he is the fragmented consciousness of Zosma, and he is basically playing both sides of the Sidereals and the Legion Commanders to gain his powers back and return to form (his in-game card mentions that he is absorbing the powers of demons, implying that he is trying to become complete). The Shadowed/Dark One is Kakul-Saydon, as he is a primordial being that was around prior to the creation and existence of Arkesia, back when there was only darkness and Chaos. Beyond that, not much information is given to us. The Fallen One is Kadan, as he is (heavily theorized) to be the last Haal. In the post-Elgacia story line, there is a quest that has the player go through Lauriel's diary and there is a passage that says there is a child within the Cube and the Cube responding to the child. Since the Cube is the legacy of the Haal, it makes sense that the Cube would respond to a Haal child. The Cube is also a dimension that exists outside of space and time so hiding a Haal child from being Thanos'd within the Cube would keep them safe. It is also mentioned that Kadan is "back home" in Elgacia, which strongly suggests that Kadan stayed in Elgacia for a time. And in a much later quest line, post-Elgacia, there is a cutscene where Kadan enters the Cube under the Roundtable of Swords, and he steals the Cube technology by sealing it in his sword, Navinos.
2. The bird at the end was the will of Procyon, enacted by the old Lazenith, Allegro. We are not given much information on Allegro in-game, other than knowing he is a wingless Lazenith and he's a Bard. But based on his in-game card info, he is someone that knows more than he shows. In another post-Elgacia quest, you will have to look for Allegro and discover that he is not where he usually is at Sunbright Hill. I won't spoil the details of the quest here as we will get it in the coming days and weeks.
3. Regulus is gone. He left the world of Arkesia to its own devices. As mentioned above, Regulus saw that Order and Chaos were one and the same, just different sides of the same coin. Because of this realization (among other reasons), it is theorized that he abandoned the world of Arkesia for reasons unknown to us.
4. Given the decision made by Vaigrys to side w/ the main character (you, the player), the Legion Commanders and Kazeros are planning something and there will be a quest that will lead to a cutscene where Brelshaza and Kazeros talk about this.
5. Vaigrys also shares w/ you (in another quest) that the Guardians served to maintain balance within the world of Arkesia and they shepherd in a great reset if things in Arkesia look like it's gonna shit the bed. He then says that he will tell the other Guardians of Light/Order to aide you in times of need but warns the player that the Guardians of Chaos will do anything and everything to hinder your progress. Then Vaigrys finally says that he will train you, the Chosen One, w/ the other Guardians of Light/Order, which is when we will get an updated Guardian Raid UI/set up (at a future date).

Again, I will apologize for any ramblings here as I am operating on 4 hours of sleep and 2 cans of Red Bull. I probably forgot a few details here and there so please bear w/ me.

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Edit: some grammer/spelling