A little longer than a minute...
So just to explain your problem.
When you create a layout, you are effectively creating a new scene. The elements in the scenes/layouts just like any other normal scene must have unique ids.
So with your new layout only the website element has an id and you cannot give the same one to the mobile layout.
We need to code around this problem.
Lets name the mobile element's id mobileCounter
And name the Website's id websiteCounter
Now with the Mobil layout selected, Go to the Scene inspector.
2, Still in the Scene inspector. scroll down to Custom Behaviors** and Add a new Custom Behavior.
Repeat the steps above for the web site layout and use the name websiteCounter.
Now in the runTimer().
At the very top of the function ( as first line) add this code.
window.customBehaviorName = event.customBehaviorName;
Then change the line:
hypeDocument.getElementById('countTimer2').innerHTML = days +':' + hours+':' + minutes +':' + seconds;
hypeDocument.getElementById(window.customBehaviorName).innerHTML = days +':' + hours+':' + minutes +':' + seconds;
Hopefully that should be it and I have not missed anything out..