I've been struggling with Apple's stupid iTunes losing my NikePlus runs for MONTHS now. I've Googled my butt off, called Apple, went to the Apple Store, and spent on the order of 20 or 30 hours trying to resolve my iPod Nano Watch losing NikePlus runs.
I recently wrote to NikePlus support to ask for help. They mentioned "re-linking" and "re-uploading" my runs. They thought that Apple would have told me about this, but Apple didn't.
Anyway, after I had those two key terms, I did some Googling. Here's what I found at:
Disclaimer: This may not work, so do so at your own risk. It worked for me though. Glad the NikePlus people knew better than the Apple people!