I've been stumbling on the subject problem for a week as I rooted my Note 3. Here is the problem and solutions I found.
My devices: Note 3 + Gear 2
This was what I was running on my Note 3: S Health (getting the data from my mobile phone) and Gear for Fitness - getting the data from my Gear 2. It was running fine for a few months since August ,just recently, the Pedometer and Sleep data on Gear for Fitness stopped sync data from my Gear 2. I thought it was the problem from the data beling uploaded to Samsung Cloud, so I created a new Samsung Account and tried for a few more data, still, only Heart data is being updated from my Gear 2 to Gear for Fitness, but no Pedometer data nor Sleep data. I was very frustrated and and tried everything, including trying wiping out all data. I tried several times wiping data out and they just refused to be deleted. I even went to Samsung Account on the Samsung website and deleted everything and still didn't work. I was very confused as where the data was residing, was it in my phone itself or on the Cloud. Anyway, as I was googling and started playing with the S Health on Note 3, it asked me to update so I did, then upon finishing installation of the app, it asked me to update Health Service, not knowing what this is, I tried it anyway. Then everything started to click! My Gear for Fitness disappear from my Note 3, S Health sync up with my Gear 2, with all the history stored, plus, I can switch back and forth between the phone data and my Gear 2. Now I am a happy camper again and thought I would share with you all.