Okay, I finally made it back to the point in the second game where Lily/Orchid appears (had to pause to replay the first game 7 times to try and get Nimble to show up in the second game).
Apparently she’s triggered simply by her still being a part of the Society. There’s a bug that’s just been reported in the Aetherfall thread where Orchid is erroneously set to having lost her powers, so that may be messing things up in some people’s playthroughs. Also deciding to rename the Society in the first game will also bjork things up.
For reference, she first shows up during your first battle against the rift-tearing troops in Chapter 3. So if she was still part of the Society in the epilogue of the first game and hasn’t shown up at that point, something has gone wrong.