RE: Maybe I've missed something - ZFS can protect against it
Super Fast Jellyfish asks, "I copy from disc C to D (even if they are virtual) to protect from bad sectors, is the de-dupe going to point to the original data and lose the effectiveness of a disc backup?"
If your desire is to protect against bit-rot, copying data between volumes is no longer needed under ZFS, there is a "copies" clause to perform this action automatically.
If you want to protect from bad sectors with ZFS when running dedup on a single drive, you can run with "copies" property, and always make multiple copies of your disk blocks. With ZFS checksumming your data, it will detect the bad block and fix it dynamically upon discovery (or upon the next scheduled scrub), instead of subjecting the user and/or business to "bit rot" data loss, as other operating systems do.
If you have multiple disks and running with redundant physical disk setup, the copies property is not required to protect/correct from bit rot, but rather the spare disk[s] will manage it under ZFS.
The next item, you can apply compression, to mitigate the expanded disk space required with "copies" property or redundancy at the physical disk layer. This also reduces performance by reducing the quantity of data being read off the disk when there is ample CPU capacity.
What is really nice, dedup sits on top of this entire infrastructure, to increase performance, and reduce disk usage. On virtual servers, this will enable more secure data, faster performance, and massive disk space reduction requirements.
If there is a problem with user error, with unlimited rolling snapshots, you can even recover without a backup if the physical media has not been compromised..
If there is an outstanding legal question with NetApp with ZFS, it will also apply to non-production quality Linux BTRFS as well. Oracle, the sponsor of mature ZFS & immature BTRFS, is big enough to purchase NetApp, anyway.
ZFS is the Gold Standard in storage and reliability.
I am uncertain how Ocarina & Permabit deal with bit-rot on the disks or whether de-dup on non-ZFS infrastructures with (or without) multiple disks can be protected against.