Apologies for a late reply.
To put it briefly, this concept takes far more research than you've put into it. These events would have global consequences, and I'd expect you to account for all of these if the article were completed. Japan's entire history, culture, and impact don't just boil down to "extremely stylized animation, pleasurable music, and pleasant beaches".
The last file isn't very good. Is this truly a satisfying conclusion? It's not very surprising or humorous, since the reader wasn't lead on to expect anything else before. Lines like "As of writing, no country or organization named 'Japan' has been found" are funny but don't make the story worth it.
A more general issue is that the progression of events fails under basic questioning. It's hard to express this without going line-by-line, but I'll try to give a handful of key examples:
- Why are "personnel on duty to be reminded that 'Japan' is not a real country?" Are they personally exposing themselves to an infohazard? If not, why is hypothesizing about the true nature of an anomaly forbidden?
- How do you play a video game (presumably) without a controller?
- The Authority acts like the culture and language of Japan is entirely alien, when it does have common ground with other Asian cultures.
- Plus, Japanese people can write. You'd think that would get mentioned at some point.
- Plus, some Japanese people are bilingual, which would be especially common for those who were abroad at the time the country sank. (In fact, anyone who's been to Japan can tell you that they see/use English pretty frequently.)
- Plus, the Authority has an entire Japanese branch.
- The general takeaway is that if Japan sank and was forgotten, the Authority would catch on way sooner than they do here.
I may sound harsh, but I respect the ambition of your writing. Your tone isn't perfect but shows a lot of effort. Contrary to what you may think, I actually feel like sinking Japan could make for a fascinating and narratively rich split timeline. However, I don't predict you'll have the patience or skill to pull it off right now.
What I do hope is that you'll be able to write a more believable world in the future. Your drafts I've seen so far are grandiose and excessive but just don't add up to reality. There's no shame in dialing it back; small stories can be just as touching as huge ones. I hope this kind of feedback can help you plan and write better drafts in the future. Best of luck!