Sometimes when you make changes to your products, or enable a certain extension, Magento might start to rewrite all your URLs to include a suffix “-1” or some other number. Within the URL Rewrites, Magento differentiates between System URLs and Custom URLs. If the System URLs are broken like this, you should not fix this by adding new Custom URLs.

Instead, open up phpMyAdmin, create a backup of your Magento database, and flush the Magento table core_url_rewrite (so that it becomes totally empty). Immediately afterwards, refresh the Catalog Url Rewrites under Index Management. This will regenerate all System URLs.