Use Anima. Pain is a magical attack that uses the Strength stat to determine damage, and it pierces the Flan's defence.
If you have Mug, use it. Nemesis doesn't counter when mugged.
I tried using Anime but it got killed in a single turn
Thanks for the tip, but I think I've already grinded out all the level 4 key spheres I need. On the bright side I had reduced the steps to Shell>Steal>Flee