You would have to customize the select statement to exclude files that are in the specials table ...

You can customize the featured_products.php module using your templates and overrides by changing the two SELECT statements to read:
Code:
  $featured_products_query = "select distinct p.products_id, p.products_image, pd.products_name, p.master_categories_id
                           from (" . TABLE_PRODUCTS . " p
                           left join " . TABLE_FEATURED . " f on p.products_id = f.products_id
                           left join " . TABLE_PRODUCTS_DESCRIPTION . " pd on p.products_id = pd.products_id )
                           where p.products_id = f.products_id
                           and p.products_id = pd.products_id
                           and p.products_status = 1 and f.status = 1
                           and pd.language_id = '" . (int)$_SESSION['languages_id'] . "'" . "
                           and p.products_id not in (select products_id from " . TABLE_SPECIALS . ")";
And the other:
Code:
    $featured_products_query = "select distinct p.products_id, p.products_image, pd.products_name, p.master_categories_id
                                from (" . TABLE_PRODUCTS . " p
                                left join " . TABLE_FEATURED . " f on p.products_id = f.products_id
                                left join " . TABLE_PRODUCTS_DESCRIPTION . " pd on p.products_id = pd.products_id)
                                where p.products_id = f.products_id
                                and p.products_id = pd.products_id
                                and p.products_status = 1 and f.status = 1
                                and pd.language_id = '" . (int)$_SESSION['languages_id'] . "'
                                and p.products_id in (" . $list_of_products . ")" . "
                                and p.products_id not in (select products_id from " . TABLE_SPECIALS . ")";
I think I have that right ...