When code is run in an ArcGIS Notebook that produces an output file in the /arcgis folder of the Files pane the file is not persistent; it disappears after the kernel is disconnected or some other action occurs. This is specific to this folder, which is apparently a location for temporary files only, even though it is the location that the Files pane opens to.
Imagine if anything I saved to my Documents folder on my local machine wasn't saved, but files within any subfolders were saved.
If users are not to generate content in this space then it should be documented as such, produce an error when code attempts to save in this location, and be easier to create sub-folders.
Saving content into this location can generate other errors, and when the output is deleted the script must be re-run.