I've been looking around a bit and haven't found anything about people vanishing.
If there were indeed vanishings, my guess would be that at the moment of the restoration of the Balance, the worlds were close to merging again. Some entire parts of Arcadia were leaked into Stark. The restoration seperated both worlds properly once again, and people in the leaks were moved.
Humans being non magical creatures, being shifted from one world to another would have little consequences.
But as you said, it was mentionned nowhere that Stark people were found in Arcadia.
During the conversation with Emma and Charlie there's this:
Emma: April was gone. Vanished. If it hadn't been for the things she'd told us, I would have simply believed that she was another victim of the Collapse.
And if you speak to one of the homeless men in Venice he'll mention his wife and child disappearing during the Collapse.
Also, regarding "seeing things" during the Collapse, there's this line in the same conversation:
Charlie: This is where it gets complicated. She spoke about another world. A sort of...parallel magical dimension. We didn't believe--
Emma: You didn't believe her, Charlie. I never doubted her.
Charlie: Fine. I didn't believe her. I'm still not sure I do, despite the things I saw during the Collapse.
Which seems to imply that there were magical things glimpsed during this strange time, which doesn't jive with things simply being reset to their "proper places".
As for the science part, the magical phenomena may have been interpreted in a scientific maner. By that, I mean that scientists noticed that for some obscure reason, an object is capable of defying laws of gravity. From those observations, engineers could establish some usage. In the 200 last years that Adrian had spent as the guardian, the balance was gradually failing. Allowing a bit of chaos in the order and probably vice-versa.
RE: magic supporting scientific principles like anti-gravity - my main problem with this is accepting that the raw element/property/whatever of "magic" obeys natural laws and works in consistent, logical ways. This is not something I'm entirely willing to accept, given the equation we've been taught that magic= chaos. But on the other hand alchemists create magical potions which presumably work the same way each time with the same ingredients. So I don't know. I read that thread you linked to (thanks for that!) and I actually prefer one of the theories in there by LogicalDreamer (third page), even if it is a little rough:
As for the collapse I always thought it made sense, throughout TLJ Cortez tells you that chaos is spreading throughout Arcadia and will eventually make its way to Stark. Stark resists it for longer because of its logic disposition, however, normally any excess of logic or chaos I would assume would get channeled from one world to another. This cant happen without a guardian hence the buildup of chaotic stuff in Arcadia, as soon as a guardian is restored, logic must be taken from Stark to Arcadia and chaos to Stark in order to balance everything out. If a crap load of chaos suddenly gets channeled into a world of logic, its not suprising that logical devices, technology, messes up. It is also mentioned in dreamfall I think that technology cant function in Arcadia without magic due to the chaotic nature of the world. Therefore, it is probably taking a while to filter out the chaos elements from Stark, which would explain why technology is taking a while to get back to normal.
Ooh, I have an Unresolved Question: How did April get back to the Journeyman from the Dream Chamber?
I'm not going to add this one simply because I think a plausible enough explanation is: the same way Zoë did it. AKA April walked all the way back around, (all the way) up the ladder, and hit the right combination on the wall. Though who knows?
when I was fiddling with 4k DSR in dreamfall, I noticed the white one saying she's all alone. But in the first reveal trailer from DLC she directs herself to Zoë again and saying "where have you gone to dreamer, the skygod has been searching for you".. so it mean she started comunicating with eachother again ?
That is really weird. I agree, it does sound like the White of Kin - isn't she supposed to be devoured right about now? Maybe the "sky god" is someone we haven't been introduced to yet? Maybe it's referring to the ultimate creator who/that exists in the Dreamtime - the Vagabond? Maybe it's the new Mother who's speaking? Regardless, I'm going to leave it out of my question list only because it pertains to DFC and I'm sure a whole host of questions will erupt as soon as we get into the actual game.
One last note - I actually replayed TLJ (and now Dreamfall) in the past few weeks in preparation for DFC and I encountered some new questions from TLJ (this original list was actually made back in 2009) so maybe I will go back to add them in if/when someone has some other contributions/corrections to make.