Force rebuild of aggregated css/js
In D7 you might want to clear also the variables drupal_js_cache_files and drupal_css_cache_files:

drush vdel drupal_js_cache_files &amp;&amp; drush vdel drupal_css_cache_files


Other than that, do you have any other cache on top of drupal (varnish?). Your pages could be cached with the reference to the old JS files. Is your site broken (404 on CSS/JS files) or is it just referencing the old ones? Usually drupal regenerates aggregated files if it can't find it.