User blog comment:Aegis Runestone/Does anyone else dislike Lucy being... *spoilers*/@comment-3338401-20120415082755/@comment-4115686-20120416030552

That is just your interperation of Juno's comment.

As for Lucy missing in Brotherhood, I believe if you go outside to catch some artifacts, and come back after a couple of minutes, Lucy will be standing outside. Desmond and Lucy will have a tender moment then.

I don't remember anything about her Abstergo passwords working in Brotherhood.