If you want to remove all the countries(options) and add only one country in dropdown located in forms(traveller info, biling address forms) in checkout page, please add following given code in functions.php file of your child theme.

function wp_travel_customized_countries( $countries ) {
  return array( 'ZA' => __( 'South Africa', 'wp-travel' ) );
}

add_filter( 'wp_travel_country_list', 'wp_travel_customized_countries' );

Before:

After:

Also, regarding creating child theme, please refer link.

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