To upgrade from 1.2 to 1.2.1, you can delete all old files (1.2) including qa-config.php file, copy new files (1.2.1), rename qa-config-example.php (new one) as qa-config.php and edit this file by adding the database details (in the new qa-config.php file). You can do the custom changes in other new files. You can use a file comparison software, if you have forgotten the changes you made.