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I've heard other people say that, but I think it's only partly true--I recently successfully upgraded my kindle without reverting any of the multiple changes I had made in the root fs (including even system scripts being deleted or replaced with links). I haven't done any testing, but I suspect that the update procedure only checks files if they are going to be replaced with changed versions. But anywhoo... just wild guessing here. Idollar is absolutely right that you should keep a record of any changes you make to your kindle after a mntroot rw.
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