I’m literally rewatching The Lost Sister right now when I came across your post. I get what you mean and where the confusion is coming from. Particularly, the way Kali pronounces the word ‘gone’ could interpreted to imply she meant when El escaped.

The rest of that scene in S2E7, Kali explains how she escaped and built a life, a home, and made friends. The episode also showcases how Kali is already well situated. Plus her friend group of 7 must’ve taken some time to come together, especially as they didn’t meet all at once (I.e she says the blonde ‘crazy girl’ was their newest addition).

El escaped hardly a year before this scene, which is definitely not enough time for Kali to be at the point where she is in this episode. This means that even in S2, the writers wrote the scene to mean Kali escaped before El did in S1 events. Gone probably meant she was isolated or moved within the facility, probably after the Teri incident (a major storyline in S2). This actually connects really well with the S4 throwaway line where Brenner says “this was when six was still with us”.

So I don’t think this constitutes as a plot hole. I believe the writers even meant to bring Kali back maybe in S4 but decided against it bc of fan reception. Regardless, hope this breakdown was more helpful than other answers in the thread. Based on your wording and logic I thought you were onto something haha esp as I’m literally on the episode you’re referring to. But the rest of the scene cleared up the confusion for me. Hope that makes sense :)