I can only vaguely remember what I had in store for Painful Past, and I just made up some of this on the spot. To resolve everything--
-- Like I said, Lupus was an anomaly. She wasn't supposed to exist, and she throws off the fabric of time and space etc. simply by existing. Her free will, if strong enough, can change what has happened or what will happen, such as in how she revived the pack.
-- Her pack was the one that stood over Quent's burning house and caused him to hate wolves.
-- (WOLF'S RAIN SERIES SPOILER ALERT) Once the Nobles have opened their fake paradise, her will to stay with the pack prevents the progression of the world's rebirth. I'm not sure how exactly that was going to work…
-- Consequentially, she must die by her own hand to make things progress. Her death would wipe her from their memories, and things would have happened as if she had not existed.
-- She was going to have this dramatic run-off-of-a-cliff suicide where she goes over her life and experiences on the way down, crying the whole way. She goes over how she will miss each significant character (Vi, Kiba, Tsume, Hige, Toboe, and Cheza), how they made her happy ("living worthwhile"), but also how painful no longer existing in their memories will be.
-- She and Tsume were going to have a between-the-lines romance. Before she sacrifices herself, they were going to have one, quick kiss.