In case I run into this again...
During a build for a .net solution using Team Foundation Server, we got an error that said.
error MSB3041: Unable to create a manifest resource name for "NewService\WarrantyUpload.aspx.resx". Could not find a part of the path 'E:\Builds\My App\Source\Code\MyApp.WebApp\Folder\File.aspx.vb'.
What had happened was that \Folder had been accidentally dragged and dropped into another folder.