If you use the Drupal Sitemap module (also called XML Sitemap), you've probably noticed that a site upgrade will convert your search engine friendly URL aliases back to the default Drupal node URLs, i.e. /node/123, etc. This XML Sitemap problem causes URL duplication in search engines since the pathauto URLs would now be replaced by the node version.

If you are unsure or using an earlier 5.x versions, I would suggest to check your XML sitemap page to see if you have the same issue. If you find that this has happened to you, here are a few things to help correct the issue (found via Drupal). Note: I would always suggest testing on a staging site versus a live site.

Several Possible Solutions:

• Uninstall XML Sitemap and Pathauto. Then, query your database, making sure all of the referrals to XML/Gsitemap are removed (you will loose all your URL aliases written by pathauto).
• Install the latest Gsitemap module and make sure it works correctly.
• Install the latest Pathauto module. In the settings, set your taxonomy according to your previous URL settings.
• In Site Maintenance mode, set Pathauto to bulk generate new aliases. You may need to run cron several times to complete that task. Your Sitemap should now be using the rewritten URLs.

Doing the above worked well and now XML Sitemap is working as it should be. The specific Drupal versions I'm using are: Drupal 5.7, XML Sitemap version 5.x-1.4, and Pathauto version 5.x-2.0.