I backup my calibre libraries using tools external to calibre.
You have to treat a calibre library as an atomic object. That is, as a single entity that can't be split up. Otherwise the calibre library may become corrupt or loose track of books.
But you can still use tools like rsync. I like rsync, because it makes it possible to create versioned backups very fast and very compact, since only modifications has to be copied, and the versioned backups are in themselves atomic copies of a calibre library or libraries, even though the versions share copies of the book formats using hard links, to save space and speed up the sync.
It is even possible to automate the backups. This is how I do it:
https://www.mobileread.com/forums/sh...d.php?t=244228
That way I get a new fresh snapshot every time I use calibre. And each snapshot is small because only contains changes since last time. But still each snapshot is a full copy of all my calibre libraries, thanks to the magic of rsync and hard links.