#!perl

use strict;
use warnings;

open(IN, "<temp.in")  or die "Can't open file temp.in for input: $!\n";
open(OUT,">temp.out") or die "Can't open file temp.out for output: $!\n";

for (<IN>) {
   s{<X-REF REFID="FN(\d+)">([^<]*)</X-REF>([^<]*)<FTN ID="FN\1">([^<]+)</FTN>}
    {<X-REF REFID="FN$1">$2<FTN>$4</FTN></X-REF>$3};
   print OUT;
}