You seem to want an output similar to

[F1]
//*************************************/
//* Filename: Config2.c               */
//* Comment: [F2] replace [F2]        */
//*                                   */
//*************************************/

[F2]
//***********************************/
//* Filename: Config2.c             */
//* Comment: [F2] replace [F2]      */
//*                                 */
//*                                 */
//***********************************/
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where comments would be cleaned up as well and not some swapping of entire records right ? if so the case then consider:

use strict;
use warnings;

local $/='';
my %hash;
while(my $data=<DATA>){
        my @array = split(/\n/,$data,2);
        $hash{$array[0]}=$array[1];
        }
        
foreach my $key (keys %hash){
        if ($key =~ /\[F1\]/){
                $hash{$key} = $hash{'[F2]'} ;
                }
        print $key, "\n", $hash{$key},"\n";
        }

#use Data::Dumper;
#print Dumper(\%hash);

__DATA__
[F1]
//***********************************
//* Filename: Config1.c
//* Comment: [F1] is replaced by [F2]
//*
//***********************************

[F2]
/***********************************/
/* Filename: Config2.c             */
/* Comment: [F2] replace [F2]      */
/*                                 */
/*                                 */
/***********************************/
[download]