If you need a way to reference the list items after you’ve cloned them, you must use classes, not IDs. Change all id=”…” to class=”…”
If you are dealing with legacy code or something and can’t change the IDs to classes, you must remove the id attributes before appending.
$("#MainConfig").clone(false).find("*").removeAttr("id").appendTo($("#smallConfig"));
Just be aware that you don’t have a way to reference individual items anymore.