In the current version of Calibre you can export hightlights (with your notes) with deep links in markdown:
To add hightlights into a book:
- Open the book in Calibre by double clicking it.
- Add a hightlight: Select text with mouse. Click the “Add a hightlight” icon in the popup window.
- Add your notes to this highlight if you like. Click “Create”
To export hightlights:
- In Calibre’s main window right-click on a book and choose “View” → “Browse Annotations”. This will show you all annotations in all your books. But you can choose “Show results from only the selected book” to show the annotations only from the book you right-clicked on. You can also add and edit your notes in this Annotation browser.
- Select the annotations you want to export.
- Click “Export all selected” button
- Select export format. With markdown you get deep links!
- Save to a file or Copy to clipboard. You can paste the clipboard to a note-taking app that supports markdown (e.g. Obsidian), and have your your annotations, notes and deep links to the book easily available.