Let's just say Chibi-verse is too damn confusing. Nora has Volume 1 eye color but knows about Volume 3 events. Ruby knows about Volume 3, alongside with the rest of Team RWBY cause they were all shocked, Jaune apparently has no idea alongside with Ren. But if you ask me, I think only Ruby and Nora knows about this. Interestingly none of them mentions Yang's amputee nor Blake's castration. So in short, RWBY Chibi isn't canon and we should stop thinking about this.

Dude. It was just a joke on how the fandom freaked out with her death and how some pretend it didn't happen.

Chill.