When you import form any camera/ card reader or alike devices through Elements Organizer's Photo downloader and specify renaming , metadata etc options then these files become different from what was present on your device.
Photo downloader has duplicate files option, as you can see in article, Import media from cameras and card readers with Elements Organizer , but for these to be detected the next time you import again from same device, you need to set all options to none the first time you download. See following screenshot for reference:
This would keep your original files intact and would detect them as duplicate the next time you connect the same device.
Hope this helps.