I remember a shadowed child asking for her aslo, in the Severed Hand I think. I believe she said that Egenia was in the lower levels of the tower. Anyway I missed her and have progressed to Wyrms Tooth, but I must go back to the Severed Hand with items from the Arbouritum so if she's there I want to try and finish that quest.
Can anyone help me out?

She's on the second level of Dragon's Eye, in the big room in the south-east. You might have killed her by accident, since she was surrounded by a bunch of trolls and Talonite priests. Any area-damage spells will turn her hostile, and if you don't know she's there, you can easily mistake her for an enemy.

-Wrath

I found here. Funny thing is, after I finished the whole Dragon's Eye expedition, I went back to where she was and she was gone. Then I go to Kuldahar, and the Priestess there still says Mother Engenia is missing. GRRR!

She always disappears, without returning to Kuldahar. People have said that she'll be in the expansion, so maybe they'll tie her in somehow with the Barbarians in the north. We'll have to wait and see!

-Wrath