Does it cause any issue if we upload whole mybb1.6.4 , but only replace two files settings.php and config.php from mybb 1.6.3
settings.php is automatically generated if its not there so you don't even have to worry about that.
config.php has not changed between 1.6.3 and 1.6.4, you just have to make sure that you port the settings correctly between them.