How does TimeMachine store Calibre's metadata and backup files? This thread is related to the thread To recover Calibre library from backup? which is discussed also with Calibre's active community as How to recover Calibre from Backup? where theducs says: 

Restore the Entire Library folder (and ONLY from a single backup). The DB records and title folder (paths) are 1&lt;&gt;1 Pairs. which is why you never mix.

If you need books from a second backup:
1)open as a separate Library and use the Copy to Library context Menu tool
2)Use Add Books.

The first does a great job of maintaining your metadata, which might not have been inserted into the book


BetterRed says that I need to [may need] to recover your configuration data. 
I run commands in the backup folder getting no outputs:

find ./ -iname "Calibre"
find ./ -iregex "Calibre"


How can you find Calibre's OSX configuration data of TimeMachine?
To manually dig through the paths, start at
/Volumes/[TM drive]/Backups.backupdb/[drive name]/Latest.
'Latest' is an alias - I'm not sure how that will resolve on nix.

The following all depends on the alias resolving correctly, as the actual locations are not 'fixed' but each may be in a different 'dated' folder on the TM drive itself.

Assuming that resolves correctly, then the Calibre plist is at [relative refs to your current folder]
~/Library/Preferences/net.kovidgoyal.calibre.plist.

Calibre Library itself is straight in your user folder ~/Calibre Library.

Prefs are in ~/Library/Preferences/calibre.