Hi,
first, I know nothing about W2k12 Dedup vs. the DA, so I may well be entirely wrong. After this disclaimer, my stance as a backup administrator is: Of course it has to back up that stuff after rehydration. That is what you normally want: A standalone backup of the original data that can be restored (partially or completely) everywhere else. Even to an older Windows release, or to your HPUX file system if need be. So it does the right thing IMO, even if that has some weird consequences for your setup. I could imagine a crash consistent backup of the entire dedup state of a drive being possible through some dedicated integration (or an option in the DA, but that is already shaky ground[1]), but something like that doesn't currently exist AFAIK. I don't know how that could deal with a situation like you trying to restore a full dedup state of the drive from last wednesday to the drive as it is now (containing other data). That's either a merge operation of two independend dedup histories, or a full replace (losing the new data) as in case of a raw disk object restore. It takes a lot of consideration and backing up rehydrated is the only real solution to this mess IMHO.
[1] There are other options that may prevent normal DA-pulled backups from being restored partially, where nothing but a full and complete restore is possible (ISTR "Log None" will force that), so there is precedence for the DA doing something like that. To be silent about raw disk backups.
HTH,
An"just thinking aloud"dre.