Actually, I've been thinking about that specific instance of AmIOkay saying "imagine the look on Maya's face when she finally slips" and, now that we know what slip means, that can actually confirm that Maya's alive.
Either she wasn't factory reset, or the factory reset itself means a different thing. Recall that when she was gone, she popped as an egg = she shifted somewhere else. What we can interpret is that, rather than being gone, Maya Prime was gone somewhere else (to the replica of heaven).
Additionally, who else is with her waiting at the place she slips to? AmIOkay! To see her face when she slips.
It's possible this has happened to Maya alone, or that it happens to everyone (see other Futaba stuck on that other plane). Maybe factory resetting doesn't erase anything, but rather transports the individual to another plane while installing a backup on Kumon-mi. This would also make sense with the fact that NAO can recall everything using the Wishing Well, well, she can do it because nothing was erased in the first place.
Basically, Maya can definitely be saved as she simply slipped somewhere, and maybe everyone can too.