[kovidgoyal]

Since the kindle just appears as a a disk it should be trivial to write a script that scans and deletes all empty folders on it. In fact here is one:

import os, sys, contextlib

def rmdir(x):
  with suppress(OSError):
     os.rmdir(x)

for (dirpath, dirnames, filenames) is os.walk(sys.argv[1]):
   for x in dirnames:
      rmdir(os.path.join(dirpath, x))

save it as clean.py and run it as

calibre-debug clean.py E:/

replace E:/ with the drive your kindle is mounted as.