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I'm planning on doing a new clean install of iOS 9 on my iPhone because I really like to have a clean slate when changing iPhones and upgrading iOS. However, the fact that Health, Activity, and Apple Watch data isn't synced to the cloud has made this difficult this year.
Is it possible to do a clean install of iOS 9 on my iPhone and also retain Health, Activity, and Apple Watch data? Or is it only possible to upgrade / restore from backup to keep that data?
No, you cannot only restore Health data from a backup. Only encrypted iTunes backups and iCloud backups store Health.app data.
The only workaround I can think of is disabling all other apps in iCloud, because iCloud doesn't allow selective restore but allows selective backup.
You need to go to your iPhone's settings, then to iCloud and disable everything in that list except for the health app. Now we know that iCloud will only save the health app data.
Before doing a restore through iTunes you need to check the encryption for your backups in iTunes before and after installation : https://support.apple.com/HT203037
Unless you are Backup to a pc with encrypted option on iTunes Health data is not going anywhere but stays in your device hardware. So if you want to transfer or don't want to lose your health data first do a backup this way. Also please check under your settings.app>general>usage>manage local storage and find watch.app, click on it and check when is the last time your apple watch has been backed up
