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Since I usually use commercial backup products, I have not tested the configuration that you describe. However, Windows 2000 backup SHOULD support backing up any type of disk that is attached to it -- Fibre or not. It looks only on the drive level for files to back up and on the SCSI level for tape drives. The fact that the SCSI traffic happens to travel across Fibre Channel is invisible to the backup application.
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This was first published in May 2002
Storage Management Strategies for the CIO

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