It turns out the data is not really gone.
I switched from a 5 to an iPhone 6 yesterday, wanting to take advantage of the new built in features of the phone, especially motion tracking.
Then the horror of all my precious health data being gone stroke me and I came to read this post. After not seeing a solution here, I rebooted the phone and all the data was back. However, it seems to be unpacking it a bit at a time from somewhere. If you click on "Sources", then the app freezes again and you're no longer able to see the data. Rebooting once again shows the data.
I waited while the data starts to trikle down on all the dashboards I had setup and then I realize that perhaps the app is consolidating its data with the data from MyFitnessPal or Pacer or who knows which other app you had as a source.
Apple should address this bug quickly. It's annoying and scary. Imagine you learned to depend on this app for all your medical needs when you go to a doctor's visit and something like this happens. Or you fall ill somewhere and the "medical ID" doesn't show promptly to let whoever finds you know that you have this or that medical condition. At this point in time it's safer to print your medical ID and carry it along with your phone.
Apple please fix this.
Device: Apple iPhone 6
IOS: 8.1.2
Apps: MyFitnessPal, Pacer
Sources: apps feed info only. Not using motion co-processor for steps (yet). Input some of the sleep data by hand (7 days)