To protect the folder, you are not just backing up the dedupe storage folder are you?

As that is the wrong process.

Go back into your backup selection list, browse I believe under the Shadow Copy Components of the BE server, and you'll see there is a component there related to the deduplication service.  That has to be selected and that alone will protect all components of the dedupe storage folder, database, etc; allowing you to restore the folder (through a normal restore job, not connecting to a folder)

This I believe is covered a lilttle in the admin guide, have you looked in there?

Well, it's not designed the way you want it to be.  It's designed to protect the ENTIRE dedupe folder, use VSS to snap the file system, and pause all dedupe processes during the backup.

Symantec's implementation makes sense, it's no different than backing up your DATA and CATALOG folder, this is just one more thing to protect.  

Rather than protecting your dedupe folder, as you dont seem to accept the recommended method, why dont you duplicate the dedupe folder to a large formatted disk (or tape)somewhere?  The data will be expanded to original size, and you can use a removable drive or NAS, and take that offsite?