If you delete documents from iCloud Drive they will also be deleted in the respective apps. There are a couple of options to restore your documents:
- Is there any chance you have activated an automatic backup in GoodNotes to another cloud storage like Dropbox or is there any recent manual backup you made? In this case, you can import the backup file via + > Import.
- Did you recently backup your iPad to your computer via iTunes? You can try to restore your iPad from that backup and your GoodNotes files should be back as well.
- Any chance you're using a Mac with TimeMachine enabled? In this case, you could try to restore a version of your Mac before you deleted files from iCloud Drive.
In addition, you read about How should I backup my documents?