The current state of affairs really leaves some interesting conundrums for our "heroes" doesn't it
inb4 no answers
Technically, there may be 2 Maya Primes, in these Alt Timelines. Sensei and Makoto may have one, and considering the Maya in Ayane's timeline seemed to notice something was off with her, she might be a Maya Prime as well. We don't actually know who is or isn't "aware" in these timelines, or why they in particular were chosen.
It's likely that being in these timelines won't last, though, and they'll return to the main timeline, after experiencing whatever they are intended to. The supernatural stuff love their little trials and tribulations, it seems. Still, chances are, the characters won't be quite the same after this. Probably a bit more traumatized.
As for most of those questions: We'll have to wait and see.
However, I do think Nao may be behind this Reset or at least involved. The Xoanon (Nao) was at least waiting for this Reset, and Ami taking care of Sensei seemed to have inspired it:
Nao being the Xoanon and in the Wishing Well was revealed back in Chapter 3's 'Mother's Milk' Happy Event:
What exactly is going to happen, is anyone's guess, but it may be Ami centered, and Nao may be behind it.
Nao and The World/Sekai(?) are also probably still looking forward to Sensei realizing how powerless he is: