jQuery clone duplicate IDs

$("#MainConfig")
    .clone(false)
    .find("ul,li")
    .removeAttr("id")
    .appendTo($("#smallConfig"));

Try that on for size. :)

[Edit] Fixed for redsquare's comment.

Since the OP asked for a way to replace all the duplicate id's before appending them, maybe something like this would work. Assuming you wanted to clone MainConfig_1 in an HTML block such as this:

<div id="smallConfig">
    <div id="MainConfig_1">
        <ul>
            <li id="red_1">red</li>
            <li id="blue_1">blue</li>
        </ul>
    </div>
</div>

The code could be something like the following, to find all child elements (and descendants) of the cloned block, and modify their id's using a counter:

var cur_num = 1;    // Counter used previously.
//...
var cloned = $("#MainConfig_" + cur_num).clone(true, true).get(0);
++cur_num;
cloned.id = "MainConfig_" + cur_num;                  // Change the div itself.
$(cloned).find("*").each(function(index, element) {   // And all inner elements.
    if(element.id)
    {
        var matches = element.id.match(/(.+)_\d+/);
        if(matches && matches.length >= 2)            // Captures start at [1].
            element.id = matches[1] + "_" + cur_num;
    }
});
$(cloned).appendTo($("#smallConfig"));

To create new HTML like this:

<div id="smallConfig">
    <div id="MainConfig_1">
        <ul>
            <li id="red_1">red</li>
            <li id="blue_1">blue</li>
        </ul>
    </div>
    <div id="MainConfig_2">
        <ul>
            <li id="red_2">red</li>
            <li id="blue_2">blue</li>
        </ul>
    </div>
</div>

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.