Sorry for my previous message, it seems I modified it before sending it. I wanted to say:
You need to create (or modify) the htaccess.conf file in the conf directory of your application and include that htaccess.conf file in the default virtual host file of Apache. That way, Apache will load that configuration at the beginning and the performance will be better than loading all .htaccess files.
Where did you deploy your application? If you deploy your own Codeigniter app, you probably followed this guide
The guide mentions that you can modify the AllowOverride field in order to use the .htaccess files but you can also create a htaccess.conf file at /opt/bitnami/frameworks/codeigniter/conf/ with the content of all the .htaccess files and include that file at the end of the httpd-app.conf file.
I hope this information helps.