They never added her thus she was never in the orginal count.
Thats why in kh even after half the org died they still didnt change the name that should tell u something.
You forget she had a keyblade like roxas.
SPY FOR WHO I DONT KNOW BUT THATS MY VIBE.
At one point they DID, and if she were a spy and they knew it would have come after the fact.
Also it's possible that she could have found secret files or anything else that the Org didn't want anyone else knowing. Since she would most likely have knowledge of it, they'd try and bring her back and use her like they wanted to do to sora (I guess we could say the same for Roxas).