Lily White was the prototype for an artificially-engineered war machine, in a fairy's shape. Shinki, feeling that merely discarding this prototype could allow others to work on the technology concealed in Lily White, has hidden most of Lily's software under a childish fairy's personality. Lily was still such an astounding work to be rubbed out, and she was given freedom, leading a careless life so far.
However, that wasn't the case for her newer 'sister', the perfected Lily Black, a fine masterpiece that sees in Shinki a sort of distant mother/creator. Shinki had the opportunity to 'test' her abilities when dealing with insurrectors, and successfully contributing to pacify rebelling factions in Makai, and outside. Shinki, fully aware of the events concerning the incidents over Gensokyo, had far more threatening issues to take care of, such as her enemies' weapons (some of their most devastating ones being Cirno, the Dragonslayer, and Rumia, Yukari's master), who are always regarded as pushovers... until the usual heroines become busy resolving incidents somewhere else.