After aiding in the destruction of the Archdemon, Morrigan
disappeared for a time. She resurfaced in a most unlikely
place—as royal advisor on mystical affairs to the Empress
of Orlais. Pg 78
Lack of comment of events during witch hunt deliberate? The warden finds her after she has disappeared, and sees her vanish through the eluvian (or possibly joins her - those still romancing have the option).