If you’re backing up your iPhone to iCloud Backup, then those backups are encrypted and include the Health app’s data.
If you’re backing up your iPhone to iTunes on your computer and you are not encrypting that backup, then your Health app data is not being backed up. And neither are your saved passwords, Wi-Fi settings, or Web site history.
While Apple doesn’t make this clear enough in my opinion, the fix is fairly simple.
- Connect your iPhone to your computer
- Start iTunes if it isn’t running already.
- Select your iPhone in the iTunes interface.
- In the Summary panel for that iPhone, located the Backups section.
- Ensure that This Computer is selected.
- Click to place a checkmark in Encrypt iPhone Backup.
- Click Sync to initiate the backup.
IMPORTANT: During the sync process, you will be prompted for a password for your encrypted backup. Do not forget this password. You cannot recover the backup without the password.
Now check that your backup completed successfully.
- Click the Edit pull-down menu.
- Click Preferences…
- Click the Devices tab.
- Look for the entry with your iPhone’s name. Check that the date coincides with the most recent backup. And ensure that a lock icon is present on that line entry. The lock means that backup is encrypted.