Update – This Technet article has more information on installing KB3216755 as a critical bug fix for Windows Server 2016 Data Deduplication users

Server 2016 and Veeam users, an issue regarding NTFS volumes with deduplication enabled has recently arose. According to a Veeam Forum Digest, there has been reports that backup files residing on Server 2016 NTFS volumes with data deduplication enabled are becoming corrupt. The reports have indicated that large files (> 2.2TB) residing on these volumes are affected. It appears that Microsoft is aware of the issue and working on a patch. A few contributors have noted that there is a package in pre-release preview to address the issue (KB3216755). Current workarounds include moving to a ReFS volume or disable deduplication. Veeam has a thread on the issue.