Just a reminder when installing 3rdparty software on MacOS.

Starting with MacOS Sierra 10.12, run:

Starting with MacOS Catalina 10.15, run:

As a note here:

Go to Menu –> Store –> Check for Available Downloads, to refresh your iBooks login manually. Also make sure the iCloud option for iBooks is enabled in settings.

Updated July 4, 2022: On MacOS 12, Go to Settings –> Apple ID —> iCloud Drive, disable and re-enable the iBooks sync. If this does not work, logout and re-login the Apple ID.