Why did the Torah keep the version of E, that Yitzchak died at the Akeidah? What did the editor(s) of E-J think, did Yitzchak die or not?
What did the redactor(s) think to do? If Yitzchak survived, he did not die!
In the light of this and this, one can say the following.
According to E, Moshiach ben Yosef will die in the war of Gog and Magog, whereas according to J, he will live. It is left to history, to future history, to decide what will be. The Torah is pure; it contains both scenarios.