Quote Originally Posted by Loony BoB View Post
Fairly sure it's because she forgot her focus. Having said that, you'd think that it would sort itself out when she remembered - although the question still remains as to whether or not she fully remembers her focus or if she only remembers pieces of it, sort of like an unfinished jigsaw puzzle. Alternatively, it's possible that once you forget a focus, the brand is screwed up entirely and not even remembering it later on will repair it. Which is good for her, I guess! Solution #1 for all l'Cie of the future: Forced amnesia!
Since everyone seems to be talking contrary to what I remember, I feel unsure when I say this but I clearly recall Fang telling Vanille that she had remembered everything. That the whole "I don't remember" thing that both of them were playing was to protect the other. They both actually remembered the events clearly since they were freed from their respective crystals.

The reason why Fang's l'Cie mark goes faded is because she half-completed her original Focus. Without Vanille she never could fully awaken the power of Ragnarok, nonetheless she tried and failed. Apparently this was enough for the fal'Cie so they were turn to crystal. When they finally unfreeze, her brand is burnt because she had tried, with little success but Vanille's was still active (at least they give the impression that it was) because she never became Ragnarok with Fang, thus not fulfilling her end of the Focus. At least that's how I understood it to be.