Been a while since I messed with Linux
you might try FSCK on the device.
Or you could try a reboot of the Kindle (menu:settings:Menu: Restart) and hope that repairs the file system.
IIRC Also, be sure nothing else is accessing the kindle (that includes looking at the directories).
Personally, Windows 7 or 10 has never harmed my kindle repairing the file system.
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