If you prefer to always keep an updated notes file on disk, this setting lets Highlights automatically save your notes to a sidecar file when saving the PDF.
Open Preferences. Go to the General-pane if it is not already visible:
Enable the Sidecar-file setting:
The next time your PDF is saved (or autosaved), the Markdown (or TextBundle if it contains images) file will be written to disk. This file will have the same name and location as the PDF, but different extension (.md or .textbundle).
Keep in mind that Highlights will overwrite any changes you make to this file externally as long as it is in this location.