When you open a site on SharePoint Designer 2010 you don’t see any Lists or Libraries.
I have noticed similar problem occur when lists or libraries are corrupted or orphaned. One way to test is to go to Site Actions --> Manage Content and Structure on your SharePoint site.
After doing that in my case I got an error. Looking into SharePoint log file the error, below, did not make much sense.
"System.NullReferenceException: Object reference not set to an instance of an object. at Microsoft.SharePoint.Publishing.Internal.WebControls.ObjectSerializer.DeleteAllowed(Boolean checkPermissions) …."
I then browsed to the site using SharePoint Manger 2010 and after clicking on every single list I managed to locate the culprit list.
Now, the task was to simply delete the list but could not delete it from SharePoint Manger, then I tried PowerShell $list.Delete() that did not work and tried stsadm –o forcedeletelist that did not work as well.
Then after some Googling again found this post that provided the trick.
Finally solution was to delete the corrupted list form user recycle bin and site admin recycle bin.