Lilisette and Lilith come from two different realities. Apparently, this kinda thing happens often enough that an entity to devour the less favored realities exists -- Atomos. I think her (their?) dad would have gotten the injury during the battle of Jeuno -- so the fight we participated in? Part of the problem with trying to work things out with the timeline is that the Spitewardens are off trying to speed/screw up the progression of events. Does anyone remember when the actual battle of Jeuno occurred and what events led up to it? Was it not that the Gigas thought Jeuno was weak and decided to attack the city?
The more I think about it, the more I think the Caits originated from Lilith's reality where the war never ended, people were forced to constantly fight and lose loved ones, and people turned away from religion and Altana. We hear Lilith talk about how things are decided by people, not by an omniscient being watching from above. It sounds like Altana saw all the despair and created the Caits to steer Atomos to consume that reality in favor of our more favorable reality. However, Lilith didn't want her world and herself to be consumed into nothingness, so she and her Spitewardens traveled back in time to prevent this from happening and to ensure her reality exists. If ya think about it that way, Lilith doesn't seem all that evil, and although her methods are questionable, having grown up and lived in an era where all she's known is war, a contest between the two identical beings seems pretty logical and reasonable.
Also, as far as Lehko goes, if he's also a Spitewarden, how does the Sinhunter play into that all. For some reason, I thought she was the mother of the trio from CoP, but that might have been purely speculation on my part. But if that is the case, then Lehko can't be a time traveler. And if they are both from Lilith's future, then why would she give him the freedom to do as he wishes? I personally believe Robel-Akbel is actually Robel-Akbel, just from Lilith's reality. In the last Windy CS, Karuha-Baruha brings up the fact that the Robel-Akbel of this reality died near the start of the war. I'm guessing in Lilith's reality, he didn't die, but failed to protect Windy. As a result, he witnessed its destruction and the death of Star Sybil and everyone else. I'm really hoping he ends up not being evil because I really like his character.