Nice new chapter. :) Yuzu has You Show riding on her shoulders, lost very, very quickly to Masumi, with whom she is at odds just like in canon even if in a different way, while Masumi might or might not be from LDS still (I can't get a clear impression...) and Sora who certainly behaves as though he has come from a place with a superiority complex. I find it very, very interesting to note that Yuzu either seems to have Yuya's memories of being scorned for Sakaki Yusho or that she remembers all the muttering being directed at her instead because Yuya has been edited away from her mind.
The introspective and reflecting part after Yuzu lost that duel was a good addition too - it fleshed the frame out more, gave a better picture of Yuzu's character and situation. (In the part where you mention Gongenzaka, you skipped tenses from past to present; you might want to correct that.)
I really like this second chapter. It continues building this story with a slow start, giving nothing obvious away and nothing out of the ordinary and yet things that draw lines to canon keep popping up. It's a very good brain teaser, making me wonder if it's an echo of memories or something else. Now it seems Yuzu wants to learn fusion, there is the Miami Championship coming up and I'd bet some 'unnatural' things/people are bound to make an appearance there. The question is, how do things get there and how are they going to continue from where they are. I do hope you are going to keep with the slow start and aren't going to rush things - that seems really important for the feel and life of the story to me.
Out of the two chapters so far I have to say I liked this one more so far and it'd be nice if they continue getting better. ;) I'm looking forward to more!

This story is shaping up real good so far nice to see you included Shuzu's concern for Yuzu that's an important part of her character. So I'm gonna guess that yuya is gone and has been erased from everyone's memories which is a pretty cool idea for a fic. Can't wait to see more!

Interested. What happened to Yuya? Is Yuzu dreaming, or maybe unconscious? Please update for more!

Oh, this is interesting. It's practically brimming with potential. Yuya erased from everyone's lives (and probably all the other Yu-s too, going by the title). What are the hows and whys and whens and whats there? Oh yes, I think I like this idea a lot. Sora is there yet Yuzu doesn't know fusion. Why is Sora there? Why has Yuzu forgotten that she used fusion? Does anyone know Pendulum? Kotsu Masumi as new student? Why did she pause at Yuzu? Where did Yuya disappear to? Does no one remember him or is it like LDS's memory editing, so that there are actually still some records of him somewhere? Is his disappearance scientific or not? Has the LDS possibly a hand in it? (Is Ms Sakaki instead of Mrs. on purpose, and if then has Sakaki Yusho also been forgotten?) It's mysteries only! Yuzu just has her perfectly normal life, or so she believes, and then pebble by pebble it will (maybe) come crumbling down until it barley holds together, at which point it might or might not get a hit so hard that it scatters and flips upside down. What I feel is important by this kind of set up is to start with Yuzu's normal life, her normal day (the way you do), with established patterns and habits and a past (as you do), fleshing it all out and giving the story a pulse so to speak, while at the same time adding little things that we, as readers, notice, but that Yuzu doesn't or makes her pause at most. This would be my constructive criticism for this first chapter too: Yuzu notices/reacts too much for a first chapter. Metaphorically speaking, the holes are too big already. I mean it like this: that Yuzu was brought up short by the empty chair in her class, finding it odd but then easily dismisses it already. That is in the later part too. I find it a bit fast that her father and Yoko react that much to her staring into empty space - that they make such a big deal out of it. I guess what I mean to say is that Yuzu is honing in too fast on the lack of Yuya and the others honing in too fast on what amounts to Yuzu missing a step. Humans aren't that observant in general, and don't jump the gun at the first sign of something out of the usual behavior. What I mean here is a subtle thing, but noticeable in the overall flow, pacing and depth. I get that it's not easy to implement (if you want) what I'm pointing out, but I thought I should at least mention it.
What I overall also like is that you have solid character interaction and dialogue (both which I personally find very difficult to write), good writing, good characters and an overall groundedness/balancedness/solidness to this that I don't see that often. I think those things are very important since its from that that you are starting a story. Also for a first chapter/introduction to a plot, this was very good.
Keep up the great work and I'm looking forward to more. :)