Solution:
Place the following code in your theme’s function file.
function remove_vc_prettyphoto(){
wp_dequeue_script( 'prettyphoto' );
wp_deregister_script( 'prettyphoto' );
wp_dequeue_style( 'prettyphoto' );
wp_deregister_style( 'prettyphoto' );
}
add_action( 'wp_enqueue_scripts', 'remove_vc_prettyphoto', 9999 );
I have tested this on my installation and it works flawlessly.
What it does is dequeues and deregisters the javascript and stylesheets that Visual Composer enqueues and registers throughout the plugin’s PHP files for the various template elements and shortcodes that use the prettyPhoto lightbox.
The ‘9999’ parameter enforces that the dequeuing/deregistering happens well after any enqueuing or registering took place earlier on in the loading of the plugin. Any number will do, but the higher the number the better.