It was actually a NTFS issue and not a dedupe Issue.
From Gostev's Digest:
Good news for Windows Server 2016 deduplication users, but bad news for all NTFS users. Microsoft has finally nailed that phantom data corruption bug that I talked about here before. We actually had quite an exceptional experience working with Windows dedupe team on this bug – they were treating one extremely seriously from the start, and it was one of those rare cases when they pushed us for updates - and not the other way around. So it made me smile when in the end, it appeared that the bug was not even in the dedupe engine, but rather in the NTFS sparse files implementation. As such, Windows dedupe gets to keep its name clean – however, the update is strongly recommend that all NTFS users, and will be included in August "Patch Tuesday". And most importantly – anyone with "Volume bitmap is incorrect" chkdsk error on your NTFS backup repositories, be sure to perform an Active Full backup after installing this patch, because you current backups may not be good. And apply the same logic to any other data that uses Windows dedupe or sparse files (create a new instance of the data).
This includes the patch: https://support.microsoft.com/en-us/hel ... -kb4025334
Ps. Dedupe should be coming to ReFS sometime...