The below MySQL Query can be used to bulk disable Countries in Opencart. The built-in process for doing this is to manually open each Country via the Opencart Admin Panel (Admin > System > Localisation > Countries).
Based on a standard Opencart installation (using oc_ prefix for Tables and opencart database name) the below Mysql Query will disable all Countries, you can then simply go to the Countries that You require via the Admin Panel and enable these.
mysql -u root -p opencart [enter mysql root password] UPDATE oc_country SET status=0;
Browse to your backend (Admin > System > Localisation > Countries) Enable your selected. Country