Usually it can be fixed by restarting the device to reset the iCloud daemon, and then leaving GoodNotes open for a few minutes with a working Wi-Fi connection.
Please also check whether the followings configured correctly:
- The device is logged into the correct iCloud account in Settings app > iCloud.
- GoodNotes is allowed access to iCloud in Settings app > iCloud > iCloud Drive.
- Inside GoodNotes, "Use iCloud" is switched on in Options > Settings > iCloud.
- Check that your documents are listed in Settings app > iCloud > Storage & Backup > Manager Storage > GoodNotes.
- The device has a working internet connection.
If the documents are still not syncing, please also take a look at this workaround.