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