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Does any one use Remote desktop and will it interfere with Pro Tools?
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Yes and no, respectively.
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Can I do thier updates for them from here?
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Only if their system has a public IP. If they don't have a public IP, you need to setup port forwarding with NAT.
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I would hate to have remote desktop crash both their rooms.
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Unlikely. I have
never had Apple Remote Desktop crash Pro Tools.
Depending on what kind of updates you want to do, working over VNC may be sufficient. Just make sure you do it via SSH so the traffic can't be sniffed.