See the FAQ.
Calibre's library folder(s) is for Calibre only, and not for you (except by way of Calibre's UI, obviously). Don't go in Calibre's library folders. Just pretend they're not there. If you want to open/manipulate ebook files directly, use the Export/Save to Disk feature, which gives you copies of your files with paths customized to your heart's content.
But don't use Calibre's library folders directly. It's bad.
Well, except if you want to back them up. Then you can do that. A lot, please.
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