use strict;
use warnings;

my $template  = "index.txt";
open(FILE, "+<$template") or die "Could not read $template: $!\n";
local $/=""; ## Or even chop $/;   !!!
s#(<% INCLUDE file)(1|2)(\.txt %>)#"$1".($2%2?"2":"1")."$3"#eg, $/ .= $_ while <FILE>;
seek(FILE,0,0);
print FILE $/;
close(FILE);
exit;