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OK, do Sync and Check for New Items still work if Calibre changes the file names?
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Since you only seem to be looking for a disaster backup of your books in case Amazon ever remotely deletes them, your Sync and Check will continue to work as it does now. In the event that you
do experience "remote deletion," it won't really matter that the filenames have been changed since there will be nothing on Amazon's servers to synchronize
with ... OR re-download (for the missing titles).