I'm wondering if there's a way to clean orphaned files from a Kindle using AppleScript or Automator.
It would basically look for any .sdr folder that doesn't have a matching .mobi or .azw and then move it to the trash.
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If the .mobi and .azw files are directly under the .sdr folders, try running a command like this in Terminal:
cd /containing/folder;for d in *.sdr;do ls "$d"|grep -Eq '\.(mobi|awz)$'||echo rm -r "$d";done
echo to actually delete the folders.