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Mark,
You have to start backing up your calibre library... including the metadata.db file. This is where all the series, tags, etc info is stored. Just back up your entire calibre folder (the one that shows in the config dialog "Location of ebooks")
When ever you send to device calibre will create the collections. So, that should be your backup. If you do that rather than worry about backing up the collection files on the reader somehow.
BOb
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