The issue is that you can't re-add a feature using an ID that you have already used until all references to it have been released. This is usually done by the internal garbage collector - but you can also force it by calling release() on the object you are deleting. This ...
Permanently deletes an object, allowing its ID to be reused. Attempting to access the object once it is released will result in an error.
Also when an object is created with the API the object does not have a base address. In this case, the object can be returned by passing only its ID to getElementById(). This can then be used to remove the feature.
e.g.
function remove(id) {
ge.getElementById(id).release();
}
Really though I would look to avoid using IDs altogether and would simply keep a variable that points to the feature, then use that to remove. e.g.
function add(fileurl) {
var link = ge.createLink(''); //no id
link.setHref(fileurl);
var networkLink = ge.createNetworkLink(''); //no id
networkLink.set(link, true, true);
ge.getFeatures().appendChild(networkLink);
return networkLink;
}
var link1 = add("http://yoursite.com/file.kml");
var link2 = add("http://yoursite.com/file2.kml"); // etc...
// then to remove, simply...
link1.release();
link2.release();