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The exported directory over USB is not the root directory (/), but /mnt/us, therefore you see the directories under it, and not /opt, /usr and the rest of the directories under root.
If your update fails because of some files you changed/removed, your easiest option is to install jailbreak and usbnetwork again, and then ssh into the kindle, check the log file for the problematic files, and restore them.
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