call reset function before populating timeline with new data (before calling my_timeline_obj.init(my_timeline_config);)

example 

make global:
var timeline_config, storyjs_embedjs;

//in your init function :
if (storyjs_embedjs === undefined) {
    storyjs_embedjs = new VMM.Timeline('my-timeline', '100%', '100%');
    storyjs_embedjs.init(timeline_config);
} else {
    storyjs_embedjs.reset();
    storyjs_embedjs.init(timeline_config);
}