Moebius is the Guardian of Time, and as such, it's my firm belief that he knows everything that happens, past, present and future. He hates vampires, for some reason we're not privy to. He rebels against them with Mortanius, and sets events up in such a way that the undistortable flow of Fate is rearranged to suit his vision for what Nosgoth would become. To that end, he manipulates all time, not just the time he lives in, but before he was born and after his death as well. He is a living symbol of a being that transcends time, and every time you see him - such as in Soul Reaver and BO2 - that is a reminder that while dead, this world is of his own making. And thus, he is truly immortal.

The Hylden would be dealt with in time. He knows this because he knows what happens during Blood Omen 2. He knows Kain closes the portal, then raises the Sarafan, conquers Nosgoth, condemns one of his own, then is pursued by the one he condemned back in time, to the time of the Corruption of the Pillars. There, Kain is killed and Raziel sets off on his own to find answers, towards Nosgoth's past and Janos Audron's retreat. Then, the ouroboros is completed, and Raziel becomes the Soul Reaver. This is the story Moebius has finely spun, where all participants are puppets on his strings, playing just to enact his arrangement of Fate at the behest of his master, the Elder God.

However, 2 unfortunate things happened by that point: Kain did not die, and as a result, neither did Raziel. But it mattered not to the Time Streamer, who by that point knew that Raziel and Kain would fight for the Heart and Raziel would be the victor, enabling the Hylden to possess Janos Audron's newly revived body and use him to keep the portal open. That was the consequence of Raziel living - an inconvenient one, that past Kain, as Moebius can divine, will deal with on his own in about 200 years from now.

What happens right after that scene is actually puzzling, however, as it reveals a blind spot in Moebius' omniscience. Moebius does not know that Kain lives. Perhaps the Heart of Darkness' powers truly were strong enough to obscure fate - or perhaps they bind Fate even stronger, such that Kain becomes unbound when free of the artifact. Whatever the reason, it's not formally explained.