Some of my own theories are pretty similar to most of the one the others have already put down here. But I've also been thinking if what if they're in one of those scrapped memories that end up getting reset? It's like in that movie Source Code if anyone else knows the ending to that.
In the ending the main character saves the people on the train in an alternate simulation world and on his last minute his life support was shut off just as he reached the last of his time limit of being in the simulation. As that happened hi lived on in an alternate world, in the simulation.
However I don't think that's likely. What I do think is someone is manually altering the world they're in (if their world takes place in a memory canvas) so that a specific thing would happen in the future. Eva's diary does say she feels like she's being followed, meaning this has been going on for quite a while now. (Note that Neil at the end of TtM taking his painkillers where the screen flashes red could represent being in a memory or just a metaphor for pain.)
If what's really happening is that Eva and Neil are both using the memory machine on themselves, (Seeing how there's only one person with a helmet in both cases.) Then the fact that there are people opposing the Sigmund Agency, perhaps Eva in the future with the helmet on might have been regretful for ever working there. Or maybe in the future the agency was shut down and she kept one of the memory machines and used it just as Neil was trying to.
Neil seems to be persistent and protective over whatever he's planning to do as if he's doing something forbidden. When you go turn the power back on as Neil and to the meeting room and interact with the memory machine there he mentions it as "could've been a miracle" in an unsatisfied manner. (Is it just that he knows the capabilities of the machine yet they're forbidden to use it that way?)
And to whoever mentioned that butterfly effect thing, yes someone might be preventing Neil from ever succeeding at his experiment and it seems to be him 8 minutes ago. When he went on hitting Eva with a broom in the face, he said that the door was locked. Why would Eva lock the door behind her if she's expecting her family, Rox and Lilly's family to come inside?
I've just realized something. What if Eva already went home and it was the doppelganger seen in the street that materialized her family and Lily's to the agency? If the door was locked, which Neil noticed, and then the Eva who was hit with a broom was the Eva sitting on her chair in a room? Since she asked why Neil turned the power off and on, she might not even be the Chair Eva from the future. It's possible right?
Whatever reasons that someone is altering that memory, it must've done something drastic in the future. However it seems illogical to change a memory to prevent something from happening in the real life unless Neil discovered that the machine was reality-altering device all along.
Whatever this is, I think this Neil and Eva side-plot won't be resolved in Finding Paradise assuming the series will be a trilogy or longer. I have a feeling that Kan is carefully planning out these plot holes for the grand finale.
Other things I noticed:
-Why was the ambient sound player recording in the ending?
-What was Eva going to say to Neil that "If you want..."? (I actually think that she's considering inviting Neil to her place in this part.)
-Neil Being speechless about Eva's diary entry seems suspicious.
-Are someone's footsteps heard exiting the basement, or was someone entering the lobby?
-Does the exit door naturally make no sound while opening and closing, or did someone just phase though the door but was still able to leave snowy footprints and loud footsteps?
-And also, cool window wiper at the beginning. So all the windows in the building have that installed?
-That sound file from Quintessence was hilarious.
Well this was a long post.
