Synchronization Creates Duplicates?

I indexed a folder and later made changes to it (just moving files into other folders). When I selected Synchronize from the file menu, it syncrhonized the moved files into the new folder locations, but it also left a copy of the moved files in their original location (the file name is blue so it is a duplicate). How do you syncrhonize the folder so it appears in DT exactly as it is in the Finder and does not create duplicates that don’t really exist in the Finder?