|Dedupe does not change data any more than compression changes data, or traditional file systems change data. Plain old LZ compression gives you a different output bitstream than what went in, with redundant parts removed, just like deduplication. But when you decompress the file, you get your exact original bitstream back. No information is lost.
Conventional file systems break up files into blocks and scatter those blocks across one or more disks, requiring complicated algorithms to retrieve and reassemble the data. Dedupe is no different. Nonrepudiation requirements are satisfied by the reliability and immutability of the system as a whole, deduplicating or not.
Jered Floyd, Deduplication is Not a Crime