TThis works in OS X 10 sierra
I had identical problem. Could not find the iBooks files in the time machine backup folder in finder. That's because the library directory is hidden. It's there you just can't see it. Using the go and go to while holding option reveals hidden library files but only in the home directory. This would be easier if apple just had a show hidden files option, but no such luck so....
Open finder and navigate to your drive or storage device that has the old time machine directories in it. Use the most current date of backup you have that would still have those books and pdfs.
Now...
Launch a terminal window.
Execute the following pair of commands: Cut and paste these 2 lines in terminal
defaults write com.apple.finder AppleShowAllFiles TRUE
killall Finder
This tells the finder to show hidden files, so that they’re displayed.
Now go back to finder and you can see to navigate to the directory ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books where the backed up version of the iBooks are. You can copy those to your desktop and then add then back into iTunes and sync back iPad iBooks
Once you have them safely on your desktop go back to terminal and do these reversal commands. Again just cut an paste lines below...
defaults write com.apple.finder AppleShowAllFiles FALSE
killall Finder
This puts finder back the way it originally was.