We have a debug mode to resolve errors with page data. To enable it, open the MCP file and set $debug = TRUE. The Structure CP will now have a “Debug” button. It does a few data checks, as well as remove any of the extraneous entries and corrects your pages lft/rgt values through a cleanup script.
You can do it manually by updating the specific entry_ids in the DB table exp_structure with lft and rgt values at the very “bottom” of the tree, so they become the last pages. So if the highest rgt value is 50, set them to 51/52, 53/54, etc. Then just drag them back to where they belong in the Structure interface.
In rare cases, a config.php error has presented itself from an older version. Open config.php and remove the $config[site_pages] COMPLETELY if it exists, clear your cache, and try again.
Backup first, of course!
