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if ($#Terms > 0) {     
    print "HERE\n";  # to confirm this takes place;
...
for (my $i = 0; $i<=$#Notes; $i++) {
    print $Notes[$i]->{terms}.$Sorted[$i]->{terms}."\n";
}

HERE
1008 1008
...
12
12
[..etc: nb, there is never anything other than 1 or 2]