Okay, I'ma go in depth with this a little bit.
So. In the main story, we are shown that Humanities resurrection is carried out in phases. Specifically, in the time with Ivy and Vanessa 2, it's shown that the architects are rebuilding humanity, and They have never even met humans. Ivy and Vanessa have to constantly speculate ideas as to what humans might be like, only having Cytus records to go off of.
This means, by the time OG Vanessa is gone and turned into Cytus 2 Vanessa, humanity is not out of cryostasis yet. But it is heavily implied in Alive: Buried that she did, absolutely, destroy all the other Operators. And then, presumably, herself as well.
By the sheer fact of what happened to Vanessa herself, we can tell what happened to them all. Cytus 2 Vanessa only has scant memories of her old self, but it is shown to be the same core, if not the same person. Their bodies and basic functions were repurposed from Operators to Architects.
And with the side story of Hans, we see this is a key distinction. Hans is an Operator. Designed to basically be a pre-existing human in a mechanical body. Architects are not that. In fact, aside from Colin himself, most people don't even know Operators existed at all. He talks about it like a rare, niche field of research you only get when doing the kind of shit he does.
This means that, the framework that as used to recreate humans was repurposed to make the Architects. And the Architects have only one clear goal. Rebuild the world for humanity.
They are not supposed to be sentient. Given the protocol outright does not allow for such sentience, it means Vanessa distinctly did not want the Architects becoming a new flavor of Operator. And yet, all the things that made them human are still in there, so it was inevitable in the end.
Then the Purge happened, and this initial wave of Architects, Like Ivy and others, were lost. And then later, a second group was made. This is the one Rin is a part of, and they actually did get to work with humans. But were still usually treated as if they are mindless robots, with sentience as a side value. Any that do awaken sentience are considered anomalies or glitches, and it's usually seen as a problem.
We can come to the conclusion that, as OG Vanessa was the one setting up this entire thing, as she's the one setting up the conditions for there to even be Achitects, that she set all this up as well.
Meaning every single bad thing that occurred to her latter self and every single other Architect is in part because she did this. Was it done out of malice? Unlikely, but after her crisis she probably didn't look very kindly on the sentient robot thing. She was likely just trying to ensure nobody tried bringing back Operators, unaware that the 'operators' themselves might try coming back.
All in all? Extremely tragic.