Why are some iCloud Drive folders missing from my backup?

What looks like one iCloud Drive folder is really several separate, individually protected locations. Apple requires that you give Parachute Backup access to each one, and no app can work around that.

Documents from apps like Pages, Numbers or Keynote live in their own app folders. Add each app whose documents you want to include under App Data in Source Folders.

On Mac

On the Mac, Desktop and Documents also need to be added separately. The iCloud Drive entry only covers the files at the top level of iCloud Drive.

On iPhone and iPad

On iPhone and iPad, the iCloud Drive entry already includes Desktop and Documents.