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If you just use python-level file access with full filenames, I don't think the notebook ever gets a chance to copy the file, because it will never know of its existence. I don't think the notebook goes digging into the python memory process just to save the data.

You might also try if setting the environment variables TMPDIR or SAGENB_TMPDIR before starting the sage notebook has an effect. According to the documentation of "notebook" it should affect the location where data is stored that needs to be transferred between the notebook server process and the worker process.