The only thing in user visible storage that a fresh cold-start can not recreate are the voice view files.
You will have to re-install them from Amazon packages if your model requires them (and you want to use them - having them missing causes no harm).
https://www.amazon.com/gp/help/custo...deId=202199580
*) Erase everything seen over usb connection
*) Remove usb cable
*) Restart the Kindle (20+ second hold of power key)
Start up will rebuild everything it needs.
PS: All of this work, before and after this post, will probably not "fix" your Kindle. You will most likely still have to send it back to Amazon.