Lost ALL Health Data

That information is provided in support documents regarding backups, such as this one. About backups in iCloud and iTunes - Apple Support

iTunes backups

From your Mac or PC, you can make a backup of your device in iTunes. Syncing your device with your computer isn't the same as making a backup.

An iTunes backup includes nearly all of your device's data and settings. An iTunes backup doesn't include:

• Content from the iTunes and App Stores, or PDFs downloaded directly to iBooks
  You can back up this content using Transfer Purchases in iTunes.
• Content synced from iTunes, like imported MP3s or CDs, videos, books, and photos
• Photos already stored in the cloud, like My Photo Stream, and iCloud Photo Library
• Touch ID settings
• Apple Pay information and settings
• Health and Keychain data
  To back up Health and Keychain data, you'll need to use Encrypted Backup in iTunes.

Find your iTunes backups on your Mac or PC and learn to delete backups that you don't need.

My emphasis added.

As the Health app is designed to be a conduit between a variety of apps, you can also use apps like My Fitness Pal, Runkeeper, and others. If you set them to read data from the Health app, you'll have information stored in those apps as well.

Unfortunately for me, I'd stopped using encrypted backups before I got the Apple Watch, because they frequently get corrupted and cause syncing to get stuck. Today I restored my iPhone as part of a carrier-approved SIM unlock, and ended up losing ALL my health and activity data from the watch. So frustrating to lose all that data. When will Apple fix iTunes' many syncing problems?

I guess a lot of it would depend on what you describe as iTunes syncing problems. The only reason that I have ever experienced with iTunes anytime in the past was a disconnect with syncing my Outlook calendar from my computer. I got that easily repaired and haven't had trouble since. You need to identify and resolve any individual problems you encounter. The saving of secure data in the backup has always been dependent on the encrypted backup.

I'm glad you've never experienced any syncing problems, ChrisJ4203. That, however, doesn't mean your experience is universal. There are documented issues where simple things such as having a duplicate song title (for example, when the same song is on two compilation albums) will cause iTunes syncing to fail -- leaving the user without a backup. Or syncing will take forever -- up to an hour. It seems to be more common when there are more apps and music on a device. Encrypted backups seem much more likely to become corrupted, in my experience and others'.

My point is that when saving ANY health data is dependent on an encrypted backup, Apple ought to ensure that encrypted backups are working. I'd also love to choose what's "secure" and what's not. To me, my steps and workouts are not so private that they must be encrypted by default.

For as many people that may experience problems, you will find numerous others that have not. I don't believe you can universally say that iTunes has issues either. Most of the time when there are issues they can be traced back to individual computer issues. The encryption is not based solely on steps, but on other Hipaa information that you would not want shared. Feedback to Apple goes here http://www.apple.com/feedback and click on the appropriate subject area.

I wish I would have read this before I did my iOS 9 upgrade or even read about backing up my watch. I just got my Apple Watch last week and the last thing I expected was to have to encrypt my back up. It would have been nice if the sales associate at the Apple store would have stressed this bit of information while I was making my purchase.

Despite all the talk of encrypted backups, I have iTunes set to encrypt but still can't recover my health data. I only have this watch because of health issues, started using it because I have had coronary surgery. What a waste!

If you have an iCloud backup, you could try that. Supposedly, Apple recently enabled backing up of health data with iCloud.

Thanks for the suggestion problem is; unlike TimeMachine iTunes backups aren't incrementally saved so if one has an automated scheduling - the last write overrules the previous one. I now have an encrypted set of empty files where my data used to be.

Jim Bailey wrote:

If you have an iCloud backup, you could try that. Supposedly, Apple recently enabled backing up of health data with iCloud.

iCloud has always backed up Health data. And it works quite well. My iOS 10 update failed to to human stupidity (mine). I restored from my iCloud back up and only lost the 8 hours of data between the last back up and the restore.