You can use EasyGPS and it's free. Save your gpx file, open it in EasyGPS then delete the duplicates, then save the gpx file. Upload that file back to your unit. You can also open the gpx file with EasyGPS then export that as a usr file. When you export as a usr file, it will automatically delete any duplicates. You can then upload this file to your unit or reimport the new usr file back to EayGPS & save as a gpx file. It sounds complicated but is is very simple. I personally like using ExpertGPS which is the paid version of EasyGPS. It has many more features than the free version but it does cost $75. I use it for almost all of my GPS organizing and editing and no I'm NOT a paid spokesman.
Have a Blessed Day,