how to remove highlight from only one selection using mark.js

Use className parameter to mark/unmark a group

https://markjs.io/#parameters

function highlightArrowsOnCheck() {
  var instanceArrows = new Mark(highlightedParagraph);
  var options = {
    "className": "arrows", // added
    "debug": true,
    "log": window.console
  };

  if (checkedArrows.checked) {
    instanceArrows.markRegExp(/\«|»/g, options);
  } else {
    instanceArrows.unmark(options);
  }
}

Working Demo

Note: togglecheckall function is simplified by triggering event programmatically.