Your problem most likely stems from different namespace definitions between the two XML documents.
For example, you might have <my:Root><my:Field/></my:Root> in two different documents, but the my: namespace might have a different definition in each
Doc1: xmlns:my="definition1"
Doc2: xmlns:my="some_other_definition"
This means that the two are incompatible and you cannot simply append XML from one to the other.
I don't know of a mechanism for redefining a namespace definition that would allow for you to then just append like you want. If someone does know of a way, I'd like to hear about it.
The method I've used in the past is to manually create XML for the second document, feeding in the values (requires code), and then appending.