You can create a backup file of your entire library in the GoodNotes Menu under Settings > Backup Data. This file can be reimported through the + button in the library and selecting "Import". It includes all your folders and GoodNotes documents.
Where is this backup saved?
When the backup process is done, the iOS Share Sheet will show up and you can select a destination or any app to save the backup file to.
Please note that GoodNotes needs to stay open in the foreground to finish the backup process.
If you close the app, the backup process has to be restarted.