We’ve seen a couple of instances of students’ Notability notes supposedly syncing to iCloud but really just disappearing. In these cases, we’ve looked closely with the students at their settings and checked both the iPad and their iCloud Drive account through a desktop/laptop computer, and—as far as we can tell—the missing Notability notes are stored somewhere in the iCloud but nowhere accessible by the user. It isn’t on any of their devices or in their iCloud Drive.
Notability has its own official iCloud sync troubleshooting steps, but the easiest and most effective solution seems to be disabling iCloud sync altogether. Once you do that and choose to keep the notes on the iPad (instead of deleting them, even though they don’t appear to exist), all the missing notes come back.
Google Drive is a better backup solution for Notability, because you can easily verify that the backups are occurring (they’re either in the Google Drive Notability folder… or they’re not). Just be sure to change the backup format from (the default) PDF to Notes.