After much serching i could not find any hidden or extra files.
When i first removed the game i right clicked the flight sim exe and then clicked uninstall, I then found the main game folder with all content in and deleted it.
I originally had the game on my main SSD boot drive and if i remember right files got put on c: like in the pic below.
I would check there and see if you have any left over files if you originaly put the game on c:
For the Japan download once it done i think you need to restart the game before it will show up.
Sorry to double post but i think the game is broken.
I downloaded the game again to see if i could help with issues and well after loading the game up and although everything looks good in my content list i also only have 2 planes to choose from now lol.
Also like the OP the Japan content don't seem to be working so gonna have a deeper dive into things.
Game was working fine for me a few weeks ago when i first installed to d: then i removed it to put it on my SSD and it all worked fine to, but i removed it from my SSD to install world of warcraft lol.
Now it's installed back to d: things defo don't seem to be working right lol, I'm also using xbox gamepass for pc so thats how i am playing the game.