Make sure you're using the latest version (4.0.8) or the latest beta (4.1.8). If you are, then LimeWire should be creating new temporary names for each one, and asking you if you'd like to overwrite the existing file as it saves. At some point in the future LimeWire will ask if you'd like to specify an alternate saved name, but for now downloading a file of the same name will ultimately erase the old one (although during the download it will have a different temporary name).