If you care about keeping a file private you would be much better served by not sending it to Amazon at all. Use Calibre or a similar program to convert and move it over yourself.
I believe that the message "the personal documents are not backed up ....blah blah blah" is simply meant to signify to you that Amazon is not a back-up service for your personal documents. That does not mean there will not be random copies of your files floating around out there on various Amazon computers.
Just as with email - if it passes through there is a very good chance that somewhere along the way a copy of that email has been stored on your ISPs computers.
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