The easiest way is to save a backup in iTunes, turn off iCloud, then restore the backup:
- Make sure all documents are downloaded locally: there should be no upload/download arrows at the top right of each documents' thumbnail.
- Tap Options > Backup All > iTunes > Upload. If the backup process fails, some documents may not be downloaded yet. Please try again later.
- Turn off iCloud: tap Options > Settings > iCloud > switch off Use iCloud > Delete from My iPad.
- Restore the backup: tap + > Import > choose backup file created in step 1.
- Make sure no files are missing and they are working correctly.
- Backup the device with iTunes or iCloud just in case.
- Then in Settings app, tap iCloud > Storage > Manage Storage > GoodNotes > Edit > Delete All (at bottom). This will delete all data in iCloud. You may consider doing this after a few days to make sure everything is working.