> [...] it seems to me that replacing a part of a XML document

> (which is what I'm trying to do) should be a straightforward operation for
> an XML database.

Sure it is. What have your tried so far? XQuery offers (actually too)
many ways to do the same thing; you could opt for replacing the $entry
variable with the XML fragment in question. Or you could use the
replace expression, e.g.

 declare namespace atom = 'http://www.w3.org/2005/Atom';

 let $old := doc('libx2_feed')/atom:feed/atom:entry[atom:id=$id]
 let $new := <node>to be added</node|
 replace node $old with $new

Christian