layer.clear() do not remove objects from the scene. It is just clear canvas element and on the next layer.draw() all objects will be drawn again.

Instead of layer.clear() you need to remove objects, that you don't need anymore. From the demo, I see that you need to remove lines and circles. You can use layer.find(selector) to find that nodes and destroy them.

document.getElementById(btn).addEventListener(click, () => {

  layer.find('Line').destroy();

  layer.find('Circle').destroy();

  layer.draw();

});