It had taken a lot of time, maturity, and reason with Lilly for her to realize what she'd told, and remembered, were almost nothing but lies. Lilith's opposition to Adam might have been reasonable by modern standards and sensibilities, but Adam's 'great evil' amounted to nothing but stubbornly wanting to always be on top when making love and ignoring Lilith's every word on the subject.
She'd quite reasonably assumed the Magical Girls themselves were the ones who were brainwashed and lied to, after all, this was true of any opposition faction. But Lilly, being a shattered segment of something greater... and thus seeing someone else's memories...
Stephanie Sparkle had carefully explained to her (whole dodging some of Lilly's attacks) that, "People remembers things the way they WANT to remember them. Memories aren't etched in stone or written in a book. They're as consistent as sand castles. They remember things the way that justifies what they want and what they feel."
And how little sense it made for shards of Lilith to want to exterminate humanity, or harvest endless negative emotions from them, if she'd been opposing an insanely evil Adam after teaming up with her 'younger sister' Eve. Or be so quick to want to destroy Lilly herself after she was granted freedom of thought and independent emotions.
Not that any of it mattered now. Now their job was to get these rejects who had failed utterly to function on a community, and turn them into cute little shock troops in a war against humanity's predators.