Then you need to load the data from the tokens file
Merge in the things you want to change
Then write the file back again
In your code you are nailing the ENTIRE file contents with the refresh token only
So something like (incomplete/semi pseudo codey)
if (res.statusCode == 200) {
const res = JSON.parse(body);
// load existing data
let tokens = fs.readFile('./tokens.json');
// override access token
tokens.twitch.tokens.access_token = res.access_token;
// override refresh token
tokens.twitch.tokens.refresh_token = res.refresh_token;
// write it all back to the file
fs.writeFile('./tokens.json', JSON.stringify(tokens,null,4));
// other stuff
}