You can rename files after download, directly in the Library pane, this will keep the current hash value that is now widely used to identify files with different names but with the same content!

If you rename or move the file in your explorer or shell, You'll need to refresh the library to see the new name, and Limewire will need to recompute the hash of contents of all new files, in order to identify it, and the renamed file will not appear immediately as a shared file in the library (this may take minutes if the file is large).