Personal opinion: The TP sages are avatars (spirit-selves) of the OoT sages. They didn't appear when Ganondorf took over in OoT because his power prevented them from being awakened.

NOTE: We know that these are avatars, because we know Rauru does not appear as such in OoT, but these sages call themselves the "ancient sages". However, I would submit that this does not mean they are all the very same individuals who forged the Master Sword; simply that they are members of the same fraternity of sages.

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