Usually this happens when the system disconnects GoodNotes with iCloud for unknown reasons. Please open the Settings app > iCloud > Storage & Backup > Manager Storage > GoodNotes, and then 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 your documents are not listed there, maybe GoodNotes was not connected to iCloud for some reasons and all documents were stored locally. Please try recovering your documents from backups:
- Backup your iPad with iTunes.
- Restore a backup from iCloud or iTunes before the documents went missing.
- Open GoodNotes (don't enable iCloud) to check whether your documents are restored. If you can find the documents, please tap Options > Backup All and then transfer the backup file to your computer.
- After it is done, you can use iTunes to restore the backup made at the beginning.
Alternative, if you have a Mac and is using Time Machine to backup:
- In the Finder app, navigate to the Applications folder in the left panel, open the Utilities folder, and then open the Terminal app.
- In the Terminal app, paste "cd ~/Library/Mobile\ Documents/5UAR78B6YU~com~goodnotesapp~goodnotes/Documents && open ." without quotes and then click Enter from the keyboard. The GoodNotes iCloud folder should open.
- Open the Time Machine app to restore documents.
If your documents are listed there with ".goodnotes.folder" suffix:
It is a bug with iCloud Drive that added ".folder" extension to GoodNotes files for unknown reasons. Then GoodNotes no longer find them because the file extensions are changed.
A new feature is added in GoodNotes 4.5 to let users fix this manually:
- Tap Options > Settings > iCloud > Copy All iCloud Data to iTunes.
- Import the downloaded documents by tapping + > iTunes > iCloud-Data.
After making sure the files are restored correctly, delete the items with suffix ".goodnotes.folder" (not ".goodnotes.folder.goodnotes") in Settings app > iCloud > Storage & Backup > Manager Storage > GoodNotes. You may want to do this after one or two months to make sure everything is working.