Im attempting to move a lot of rewrite rules from the .htaccess file to some the apache config files, I recieve no errors and placed this inside the VirtualHost portion of the sites config file:

<Directory /var/www/da/>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride All
        Order allow,deny

        allow from all

        RewriteEngine On
        RewriteBase /

        RewriteRule ^botswana/central-kalahari/$ /central-kalahari/ [R=301,L]


Rewrite Rules put into server config / virtual host context will begin with leading slash -- that's among the variations from .htaccess behavior. Therefore use that one:

RewriteRule ^/botswana/central-kalahari/$ /central-kalahari/ [R=301,L]