Unfortunately, yes! Decipher Phone Refresh creates a "filtered" backup from your original iPhone backup, for using with "Restore Backup" in iTunes.
Restoring a backup in iTunes replaces (overwrites) your existing data with the contents of the backup (and only the contents of the backup), so restoring the Decipher Phone Refresh filtered backup will replace the contents on your iPhone just like restoring a normal backup. That means in terms of data (settings, app documents, etc) you'll have only the data from the backup on your iPhone after the restore.
If you want to transfer Health/Activity data from an old iPhone to a new iPhone that is already set up, you can use iCloud to sync your Health and Activity data. To enable iCloud Health syncing, you'll need the old and new iPhone to be running iOS 11. Here's two great sources to read more about iCloud Health/Activity syncing from iDownloadBlog and iMore.