How clean we talking about here?
If you blow away the bootloader in flash then you'll be stuck if you don't have a JTAG adapter that supports 1.8V.
If you delete everything in flash then you'll lose the Kindle specific items like the Kindle ID and DRM keys and calibration data for your screen so if you don't have a backup then you're stuck again. You can't just copy it off another Kindle since the keys won't be corerct.
In theory you can recover from a bad firmware by putting the Kindle into recovery mode however we don't have any complete firmware images. The images that have been release so far have all been patches.
In short, it is possible but I wouldn't even consider it unless I had a full backup of the Kindle first and a 1.8V JTAG adapter along with software that supports the Freescale CPU and MoviNAND flash.
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