Abigail-II is completely right about wasting time of others by not supplying the real example in the first place. Secondly, please use <code>-tags; they make code and input/output much more readable.
Anyways, the following should work for you: 
#!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;
}

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In reply to Re: with better example by CombatSquirrel
in thread replacing text in specific tags by texuser74

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
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