It's hard to tell how to fix it without all of your code (HTML + JS) -- we can't see what the element with id "number" is. That said, it looks like you're just trying to append new HTML. So, replace this:
var div = document.getElementById('number');
div.innerHTML = div.innerHTML + '<div class="number-pop" id="number-add-'+ numberPop +'" style="z-index:99; position:absolute;margin-top:'+ (mainEvent.screenY - 98) +'px;margin-left:'+ (mainEvent.screenX - 12) +'px;">'+ '+1' +'</div>';
with this:
$('#number').append('<div class="number-pop" id="number-add-'+ numberPop +'" style="z-index:99; position:absolute;margin-top:'+ (mainEvent.screenY - 98) +'px;margin-left:'+ (mainEvent.screenX - 12) +'px;">'+ '+1' +'</div>');
That will add the new HTML without resetting existing elements.