That bit has long been retconned.
The story of this mod does not follow the official canon. In HTW, Hylia and Zelda are different people. The leader of the Wizzrobes is not a resurrected soulless abomination, she is the same Hylia who led the Kingdom of Hyrule 5 millennia ago, and she never died at the first place to be able to reincarnate.
Chimto
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