Google crawlers just follow the HTML. If you intend on deleting CSS&JS files, search through all your themes&plugins that were using the files and either comment off or remove the line calling the CSS&JS files.
Look for both wp_register_???() and wp_enqueue_???().
Examples for plugins:
wp_enqueue_style('wp_css_name', plugins_url( '/assets/css/style.css' ... ));
wp_enqueue_script('wp_js_name', plugins_url( 'assets/js/script.js' ...)...);
Example for themes:
wp_register_style('normalize', get_template_directory_uri() . '/normalize.css'...);
wp_enqueue_style('normalize');
With all themes&plugins not calling for nonexistent files, your problem is solved.
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