So, where Relic Song, Heart Swap, and other options are available to use with the Quartz Flute, I am only able to use Darkrai Cultist, Seed Flare, and Tesseract. The other options don't appear on the list that appears after using the Quartz Flute.
Opening up past versions of Insurgence don't fix the problem, though this doesn't happen on other save files besides the one where this bug occurred. Losing a battle also doesn't fix this.
This bug's not major all of the time, but since Heart Swap is required to finish mission 6 of the Suntouched City news station sidequest, I'm trapped in the mission until this is fixed.