This is a possible scenario that can happen with Veeam and Server 2012 deduplication:

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You cannot write to a file anymore and you get the error "ERROR_FILE_SYSTEM_LIMITATION". There is still plenty of space left on the volume however this file can't grow. This is a big issue wince you use rollback chains in Veeam.

To fix this unfortunately you need to start a whole new chain on a new volume. When formatting the volume, use format drive: /fs:ntfs /v:volumelabel /Q /L. The /Q switch does a quick format, and the /L switch enables large-size file records.

Unfortunately this switch isn’t very well documented - it’s not even in the format.exe knowledgebase article. You can however get some information from format /? in command prompt.

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/L	NTFS Only: Use large size file records.
	By default, the volume will be formatted with small size file records.

A Microsoft primer on how NTFS works (Source.aspx)) sheds some light but it doesn’t show you the limit of setting large-size file records.

Reference: Microsoft KB2891967