This usually happens to minor issues with your iCloud account and can easily be solved:
OIpen the iOS Settings app and navigate to iCloud > Storage > Manage Storage > GoodNotes. Wait for a second and your documents and categories will be listed there.
Look for the category and swipe over it to delete it. This should also delete the category in GoodNotes.
Please note that any changes you make there can not be recovered and will affect the copies inside GoodNotes.