use strict;
use warnings;

my $str = do { local $/, <DATA> };

my @fnote = qw(<FN1>footnote1</FN1> <FN2>footnote1</FN2> <FN3>footnote1</FN3>); #Already retrived footnotes

my %hash;

for (@fnote)
{
	$hash{$1} = $_ if ($_ =~ /<(FN\d+)>/);
}

$str =~ s|<(FN\d+)ref>|$hash{$1}|g;

print $str;

__DATA__
<p>
Here some text <FN1ref> and some text
Here some text <FN2ref> and some text
Here some text <FN3ref> and some text
</p>
<FN1>afsdfsaf</FN1>
<FN2>afsdfsaf</FN2>
<FN3>afsdfsaf</FN3>


outputs:
--------
<p>
Here some text <FN1>footnote1</FN1> and some text
Here some text <FN2>footnote1</FN2> and some text
Here some text <FN3>footnote1</FN3> and some text
</p>
<FN1>afsdfsaf</FN1>
<FN2>afsdfsaf</FN2>
<FN3>afsdfsaf</FN3>