I have recently had the need to merge multiple Nessus reports into single reports and here is the code I used to do it. Take care and if it breaks for you you get to keep both pieces . Please note that you need to change the report name to the same value, like this:

sed -i -e s/\<Report\ name=\".*\"\>/\<Report\ name=\"Combined\ report\ name\"\>/g reports/*.xml

mergeReports.pl

#!/usr/bin/env perl

use strict;
use warnings;

use XML::Merge;

if ( $#ARGV < 0 ) {
    print "Merging into " . $ARGV[0] . "\n";
    my $merge_obj = XML::Merge->new( 'filename' => $ARGV[0] );
    foreach my $filename (@ARGV) {
        if ( $filename ne $ARGV[0] ) {
            print "Merging " . $filename . "...";
            $merge_obj->merge( 'filename' => $filename );
            print " Done!\n";
        }
    }

    print "Tiding up.... " . $ARGV[0];
    $merge_obj->tidy();
    print "Done!\n";
} else {
    print "Usage: mergeReports.pl Output.xml inputfiles.xml\n";
}