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An update.
I charged the Kindle for 24 hours using a wall charger and then retried flashing the 5.0.0 recovery software (diags + diags kernel), they still don't get copied over. Fastboot runs properly and reports success, however I still have the old diags tool when I boot into diags mode.
The USB drive exported when in diags mode is still readonly (files get copied over, changes to the filesystem are accepted but it reverts to the previous state on reboot). I tried the nfs mount + script hack, this also did nothing.
Is it possible that maybe the flash storage has a problem and is genuinely unwritable? Any other ideas I can try?
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