You absolutely must use an image-based backup like Legato's SnapImage or Veritas' Flashbackup. These products backup and recover at the raw disk level instead of going through the filesystem. They offer file-level recovery but when it's time to restore the whole filesystem, they restore it via the raw device. These products and others like them are the only way to backup the type of system you're describing.
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This was first published in June 2002