It is better to use a separate file to prevent an overwriting during an upgrade.
Filter load_textdomain_mofile
and replace the old file with your own:
add_filter( 'load_textdomain_mofile', function( $mofile, $domain )
{
if ( 'name_of_the_textdomain' === $domain )
return 'path_to_your_file.mo';
return $mofile;
});