change $src from wp_register_script in plugins/themes

Well of course you can. All you need to find is what handle they are using for those scripts. let’s say they are uing plugin-script handle. Then you deregister and register script again with your URL. Like this.

function wcs_scripts_styles() {
    wp_deregister_script( 'plugin-script' );
    wp_register_script( 'plugin-script', get_stylesheet_uri(). '/js/jquery.script.js', array( 'jquery' ), NULL, true );
}
add_action( 'wp_enqueue_scripts', 'wcs_scripts_styles' );

This will replace script location to script hosted in you theme js folder.