iOS 10 Safari: Prevent scrolling behind a fixed overlay and maintain scroll position

Add -webkit-overflow-scrolling: touch; to the #overlay element.

Then add this JavaScript code at the end of the body tag:

(function () {
  var _overlay = document.getElementById('overlay');
  var _clientY = null; // remember Y position on touch start

  _overlay.addEventListener('touchstart', function (event) {
    if (event.targetTouches.length === 1) {
      // detect single touch
      _clientY = event.targetTouches[0].clientY;
    }
  }, false);

  _overlay.addEventListener('touchmove', function (event) {
    if (event.targetTouches.length === 1) {
      // detect single touch
      disableRubberBand(event);
    }
  }, false);

  function disableRubberBand(event) {
    var clientY = event.targetTouches[0].clientY - _clientY;

    if (_overlay.scrollTop === 0 && clientY > 0) {
      // element is at the top of its scroll
      event.preventDefault();
    }

    if (isOverlayTotallyScrolled() && clientY < 0) {
      //element is at the top of its scroll
      event.preventDefault();
    }
  }

  function isOverlayTotallyScrolled() {
    // https://developer.mozilla.org/en-US/docs/Web/API/Element/scrollHeight#Problems_and_solutions
    return _overlay.scrollHeight - _overlay.scrollTop <= _overlay.clientHeight;
  }
}())