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From the apple support channels, they suggested that the most likely cause was data corruption. The issue persisted after restoring a backup too.
 
Oh hell. I should hold still until next update. Losing health data is a pure bummer for me.
 
@Shirasaki
The thread I found above suggests that a small number of people see this issue, but clearly it isn't pervasive otherwise I would have expected more of an outcry! Hopefully you wouldn't be one of the unlucky few..

I'm going to try restoring to a slightly older backup, and if that doesn't work attempt reverting the software to the previous version and restoring the backup again. If the latter works it would convince me that it's a software issue with the new update. [Or, as Apple suggested, a software issue with the old software that has rendered the data unusable in the new version, even if it works in the old software. Unfortunately, from my understanding of their messages they'd still classify this as data corruption, resulting in loss of all health data]
 
Just upgraded now and same issue happened to me (7+).
After some search, I found someone say that if downgraded to 10.02 (or 10.03) , the health data will show just fine. Hence cannot be data corruption , right? (I'm so scared and frustrated right now)
 
After some search, I found someone say that if downgraded to 10.02 (or 10.03) , the health data will show just fine. Hence cannot be data corruption , right? (I'm so scared and frustrated right now)
Yes, I saw that in the thread I mentioned in my first post. Haven't tried it yet, let me know if it gets it working again for you! If it does, I'm thinking that one option would be to export the data as XML, perform the upgrade, then re-import it using a third party app (perhaps something like that suggested in the link below?). Some information might be lost though, not sure whether apple watch activities would be preserved.

https://www.igeeksblog.com/how-to-export-import-health-data-in-ios-10/
 
Reverting to 10.0.3 and restoring the backup seems to put everything back to normal. To me that almost certainly indicates a bug in 10.1. I'll follow up with Apple, and hopefully they'll fix the problem!
 
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