functions.php file is where you can do wonders with your theme without touching the core WordPress files. Most of the time the backup functions.php trick would work for you unless you aren’t changing anything in the database with any of your action or filter hooks. You could check this link too -> http://codex.wordpress.org/Theme_Development#Functions_File
Regarding the .htaccess – you should be fine by just replacing the backup file. Nothing irreversible done here.