Drupal 7.26 multi-site , one of my sites is playing up. Error started with no login page until I realised all nodes except home were not found. So I tried putting in code in index.php to see errors but none showed up. Then I dropped the database and reinstalled settings to start with basic drupal install but after importing sql and again drush updating database still pages cannot be found excepting home page. Then went to ?q=user to login as admin and could see all the pages but clicking on any one of them would throw page not found error.
update: this has morphed into new question but was able to regain pages by removing clean-urls so will grant answer and ask new question.