One possibility: 
#!/usr/bin/perl
use strict;
use warnings;

my %edits =
  ('AAAAAA' => 'BBBBBB f11 f12 f13',
   'CCCCCC' => 'DDDDDD f21 f22');
   
my $line;   
while ($line = <DATA>)
{
    print $line;
    chomp $line;
    
    process_section ($edits{$line}) if exists $edits{$line};;
}

sub process_section
{
   my $input = shift;
   my ($end_token, @values) = split (' ',$input);

   foreach (@values) {print "$_\n"}
   
   my $this_line;
   while (defined ($this_line = <DATA>) and $this_line !~ /$end_token$
+/)
   {
      next;
   }
   print "$end_token\n";
}   



__DATA__
aaa
aaa
AAAAAA
ccc
ddd
BBBBBB
111
222
333
CCCCCC
444
555
666
DDDDDD
777
888
999
  
=PRINTS:
aaa
aaa
AAAAAA
f11
f12
f13
BBBBBB
111
222
333
CCCCCC
f21
f22
DDDDDD
777
888
999

[download]
update: There is flaw in this. Adjacent sections will not process correctly. However this approach, with modifications, scales to large files.

In reply to Re: The best way to replace several fragments of the file starting with the one pattern(marker) and ending with another pattern/marker. by Marshall
in thread The best way to replace several fragments of the file starting with the one pattern(marker) and ending with another pattern/marker. by likbez

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