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?

Thanks