I usually use XML::XSH2 for XML manipulation. In this case, I'd use something like this:

$new := create new;
for { glob "folder/*.xml" } {
    open (.) ;
    if $new/new { # for the first file, copy the root as well
        cp shiporder replace $new/new ;
    } else {
        cp shiporder/shipto append $new/shiporder ;
    }
}
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