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I've been using FTPS via Filezilla on my Win2k3 server after a mandate for encrypted file transfer came through. I use Beyond Compare or other FTPS clients on my Windows 7 and XP boxes to connect.

Is this the fastest encrypted option for moving files to and from the Win2k3 box?

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To get the fastest you're really going to have to run benchmarks. Different means produce different results depending on the actual data being transmitted. However, I'd personally be looking into a VPN of some sort between the systems. If the data being transmitted is a "refresh", rather than all new material you should also look into using rsync or similar, so as to only transmit the changes.

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There is already a VPN that I'm going over, but it's enterprise wide, so I need to encrypt within that from server to workstation. It's largely script files. –  Caveatrob Apr 12 '12 at 3:38
    
@Caveatrob, as script files are generally quite small I don't think you'll see much difference regardless of which method you use but any method which offers compression should work best, as scripts are generally very compressible. I'd still be considering rsync (over SSH). –  John Gardeniers Apr 12 '12 at 5:39
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