Data and folders
Since Scene Notes is a purely project-based tool, the data for the notes is stored in a specific folder as ScriptableObjects. The location of this folder is initially Assets > SceneNotes, but it can be changed in Project Settings.
Data format
Inside the main folder, alongside the NoteCategories ScriptableObject, multiple folders will be created with the guid of each scene that contains notes:

As notes are moved between scenes, these folders will be automatically created and destroyed, so you don't need to manage them.
Inside these scene folders, each ScriptableObject represents a note:

The file name reflects the note's title and is automatically updated when the title changes.
When the toolbar is open, what is visualised in the scene are invisible GameObjects that reference these ScriptableObjects. Deleting one of these GameObjects will not delete the ScriptableObject.
Though notes are generally meant to be managed from within the Scene View, it is totally possible to manage them directly from their ScriptableObjects: changing properties, assigning different scenes, etc.
However, after making these changes, it's good practice to reload the notes from the Overlay so they show correctly in the Scene View.
Version control
As notes are meant to be shared across the team, the folder containing the Scene Notes should be versioned using the version control of your choice. This way changes to the notes can be pushed and pulled just like any other regular file.
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