Child themes only override php files (like header.php) that are included with functions like get_template_part or get_header, etc.
The correct way to add scripts to WordPress is with wp_enqueue_script. If your parent theme uses this, you can override the JS files by using wp_dequeue_script and enqueuing your own.
// hook in late to make sure the parent theme's registration
// has fired so you can undo it. Otherwise the parent will simply
// enqueue its script anyway.
add_action('wp_enqueue_scripts', 'wpse26822_script_fix', 100);
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