They gave her some backstory for the Crystal War, she was Cardinal Mildaurion who helped the survivors of Tavnazia get to the safehold. Plus she was the one who cast the spell on the Phomiuna Aqueducts that caused the level cap.
As for what she was doing during RotZ, I would guess that she either didn't have the power within the Armathrwn Society to stop their plan and gained power after they died, or she didn't return to Jeuno until after their plans were foiled and gained her power because she was their long-lost sister. The story does not expressly state her whereabouts, and I would hate to have to "just completely make up reasons".
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