Good Afternoon Susan,
On the javascript side you can delete all the annotations in a layer. Call the WebAnnotationViewer.setCurrentLayer(index) then WebAnnotationViewer.getCurrentLayer(). Then you have all the annotations in an array from myAtalaLayer.getAnnotations(). You can loop through them and get their Z-Index. With their Z-indexes you can delete them all individually with the WebAnnotationViewer.DeleteAnnotation(zindex) function.
~Kevin