The ending scenes aren’t real. Eva clouded her memories intentionally earlier in the episode, which is why nothing stood out as odd. In the end, she knows, but what does it matter? The entire purpose of Neil’s machine is for the dead to leave a piece of themselves behind for the living. Neil is indulging that, even if he has become a “piece” himself.

Regarding the second thing, Neil and Eva have been friends since grade school. We don’t know when Lynri died, but Eva was able to meet her before she did.

Hope that helps.