The problem seems to be not with the contents of the file, but the filenames themselves.
Hiragana, Katakana, and Kanji aren't supported well and it would be better to turn the filenames into Romaji instead.
If possible, stick only to the 36 alphanum characters, underscores, and dashes.
Afterwards, you will need to update the game to use the new romaji filenames instead of the old ones.
In that case, it sounds like there's a file that doesn't have the right encoding. It's probably the files coming from a JPN since they default to ShiftJIS.
You'll need to identify which files came from that JPN and see if the file's encoding is at UTF-8 after you use "Re-open with Encoding" in VSCode. VSCode defaults to UTF-8 even if the file isn't so you'll need to use that re-open.
https://imgur.com/a/vVpEjmA
Once you identify what files aren't actually in UTF-8 encoding, then you'll need to use "Save with Encoding" and need to save it as UTF-8 this time.
But if you're comfortable enough with command line tools, I'd recommend using iconv instead and just force everything to be UTF-8
