The remove_child() function seems to have a bug. if the parent node of the node you are trying to delete is the same as the root node it will give you unexpected errors. I fixed this by checking if the parent node of the node i was deleting was the same as the document node. take a look at the function below if you are running into the same problem. $this->xmlData reffers to the domxml object inside the class i was using.
<?php
function deleteNode($ref, $levels) {
$parent = $ref->parent_node();
$root = $this->xmlData->document_element();
if($parent->node_name()==$root->node_name()) {
$parent = $this->xmlData->document_element();
}
if($parent->remove_child($ref)) {
return true;
} else {
exit("error removing node");
}
}
?>