Hi and welcome to the GreenSock forums,
Thanks for the demo.
Please try
var mummudRepeat = new TimelineMax({repeat:-1})
var mummud=$('#mummud > g path'),mummudArray=mummud.toArray();
mummudArray.sort(function() {return 0.4-Math.random()});
mummudRepeat.staggerTo(mummudArray, 0.2, {opacity:0, repeat:1, yoyo:true}, 0.4)
by repeating each staggered tween with yoyo:true each dod will fade out and then fade back in.