I have 3 installs of calibre 8 portable - 8.0.0 (fresh download/install today), 8.16.2 and 8.99.11 - the backups of all three have empty sub-directories.
If I create a zip of Calibre Settings with Windows, WinRAR, or 7zip the subdirectories are not empty. And my installed instance is OK too…and its not even in the 'usual' place.
It's something in Settings itself - I just installed a fresh 8.00, added this PI and it's OK…
BR