I had to ask because the kindle has a mode where the storage available shows up as zero and at the same time does not show any files.
(You mentioned the one but not the other.)
My next guess is that it has something to do with the 'Readyboost' feature.
See if you can disable that or work around it somehow (like, copy the file using the command line).
Or even better yet, change computers.
Something older or something Linux or MacOSx
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