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There must be a metadata.db file on your pc. If it isn't there, calibre won't start. The file is in your library folder at the top level, the same level where you see the author folders. If you are using Windows then depending on your settings the file might seem to be named "metadata".
As for updating, it appears that the Amazon app is happy to upload new files, but refuses to upload changed files. This means that changes you make to books such as updated covers will not make it to the cloud. In addition, the calibre auto-backup files won't update, rendering them less than useful.
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