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See this article for some troubleshooting information:
Hi, iTunes uploads to Nike+ generally work very smoothly, and you should be absolutely sure about your setup as described above. But sometimes the upload of a workout to Nike+ fails, in my case typically if the connection to Nike+ was unstable for whatever reason. iTunes then responds with an "Unknown Error".
Here is a last resort if your setup is verified, but workouts are still missing: In such rather rare cases, iTunes already transferred the corresponding xml file (= the workout data) into another folder of your iPod. Then iTunes thinks that there is nothing left to upload, but the job had actually not been done.
Sync to Nike+ can then be repeated with some manual work. Use the procedure described in the below links in order to recover lost workouts from your iPod for re-syncing by iTunes:
So you should be absolutely sure that your iTunes/Internet/Nike+ is set up correctly and that you are actually missing workouts in Nike+. Otherwise you would create duplicates there. And you obviously need to know how to show hidden files in MacOSX/Windows. Then it's fairly easy to check on your iPod whether (1) the workouts are still there and (2) they are considered synced to Nike+.
It saved my 'lost' workouts in three or four cases (out of nearly 500 workouts). Just had to do it again, and it worked flawlessly. Hope this helps.