Please check whether iCloud Drive is enabled in the Settings app > iCloud. On iOS 9, iCloud Drive must be enabled for GoodNotes to work with iCloud.
If it is already enabled, please check whether GoodNotes is allowed to access iCloud in Settings app > iCloud > iCloud Drive.
Then please open the Settings app > iCloud > Storage > Manager Storage > GoodNotes, and check whether the missing documents are still in iCloud.
If your documents are listed there, please open GoodNotes again, tap Options > Settings > iCloud, and then switch on "Use iCloud". Your documents should be available again.
If not, please send us an email via firstname.lastname@example.org.