What games are you exactly referring to? I'll try to answer.How can he die in one and only be sealed in another?
Ganon was sealed the Adult Ending of OoT. He later broke free of the Sacred Realm, Hyrule was flooded, WW took place. In the Child Ending of OoT, Link warns Zelda of Ganon's plans. He was captured and was held captive until TP when he was sealed in the Twilight Realm. Whether he died at the end of TP is debatable. Nonetheless, OoX must come after a game in which Ganon died, not before.
And, as the user stated above me, FS is before FSA because Vaati actually died at the end.
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