Something that occurred to me (SPOILER ALERT):



At the end of _Skyward Sword_, Fi sealed Demise away in the Master Sword, which is basically her, if I understand correctly. What if the release of Calamity Ganon has awakened what remains of Demise, and in its constant struggle to escape, it's hurting Fi, resulting in the Master Sword decaying when it never seemed to before?



Still, I'm pretty sure she will be curable/fixable at some point. At least, I hope so.