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DFS-R & Encryption

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I understand that DFS-R doesn't work with EFS but it does with BitLocker.  What about application level encrypting?  We are looking to implement a write-once, read many file replication solution.  

In my scenario, an end-user web application writes files to the local disk.  These files are encrypted within the application before writing to disk (exact methodology unknown).  I was thinking DFS would be ideal for this but need clarification on the limitations surrounding file level encryption on an DFS-R implementation.

The back-end AD schema is 2003 R2, running at 2000 Mixed mode functional level.  The file hosting servers will be either 2008 R2 or 2012 pending further research.

Thanks in advance.


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