If you find out how the files work (game's BCAT files), then you can change the data (for a folder ->) and then edit the `files.meta` file (for that folder) to work with the files that you changed (or added).
There is this one post on someone made about Animal Crossing BCAT save and how to make edited BCAT save work:
https://gbatemp.net/threads/acnh-bcat-forging.564556/
It included an image for what the data in `files.meta` file meant too: upload_2020-5-7_11-19-58-png.208092
iirc they edited the data (it was xml or yml or something like that) -> changed/fixed files.meta to work with changes -> restored (probably using JKSV to dump and restore).
idk about the data in the root thing (na_required, list.msgpack (it has the file links and stuff like that)). Idk what happens if passphrase.bin is changed, but if it is deleted then the next time the game is launched it will regenerate. It always regenerates with the same data (I think) and I think its different for each console.
Note:
dot_ File size limit thing (total) = 60MB
the game reads the stuff like this: `directories/folder/files/file.file` -> `folder/file.file`. You can't have 2 folders (game reads example: `folder1/folder2/file.file` will not work)
I probably wouldn't try it while connected to the internet (Nintendo's servers and stuff like that). I would also backup the BCAT save so it can be restored after the testing is done so the BCAT server doesn't get confused and stuff like that idk.