How do I backup calibre?
Implies proper backup = whole folder.
The rest is experience. (Some of us have been around for quite a while, and have picked up a lot along the way, doing weird things is a learning experience.

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If there's something you aren't quite sure about -- ask!
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The metadata.db holds the metadata only, all books are kept in a (rigid) folder structure in the same root library folder as the db.
Backing up the metadata only gets you so far. It is mainly good as a unique way of
locating the correct library folder.