It certainly looks like whatever Eve encountered in that vortex has heavily influenced or outright altered her, and that this manga is streaming straight towards an ending based on the altered version. That would be a terrible narrative decision, leaving the real her with no resolution.
Imagine if, in Star Trek TNG, Data had been manipulated by Lore into being hostile to the rest of the crew, and they had responded by simply shutting him down and saying "well, I guess he was no good after all".