I've been working on a HealthKit app all summer (and have lost 40 pounds and 15 mg/mm off my blood pressure because of it), and will report on my app soon.
In the meantime, based on my (now) extensive experience with the HealthKit API's, which act as a sort of central database for health-related information, I think there are two possibilities:
- Data loss. From time-to-time with various iOS betas I've experienced problems where data has disappeared from my device.
- Leakiness. Two sub-possibilities. Either there is some side channel vector that allows unauthorized access to HealthKit data (which would obviously be problematic) or Apple just discovered some flaw in the app review system that should probably be checking to make sure HealthKit apps don't do things like take HealthKit data and put it in the cloud.
Depending on what the issue is, it sounds like an iOS point update may be required to resolve it, which could result in delay of at least a week.
Update: Looks like it was either data loss or leakiness due to side channel, since Apple is saying it may take a couple of weeks to fix via software update.