I'm not sure I'm clear on your requirements. It seems that you want to sort the matching lines but leave all the other lines in whatever location you found them.

my @lines = <DATA>;
my @matching_indices = grep $lines[$_] =~ /id:\s?\d/, 0 .. $#lines;
my @matching_lines = @lines[@matching_indices];
my @sorted_matching_lines = sort { my ($an) = ( $a =~ /id:\s?(\d+)/ );
                                   my ($bn) = ( $b =~ /id:\s?(\d+)/ );
                                   $an <=> $bn
                                 } @matching_lines;
@lines[@matching_indices] = @sorted_matching_lines;
print @lines;
__DATA__
#Comment
*ss id addr id: 099 bbb ccc aaa
*ss id addr id: 003 aaa bbb ccc
#Comment 2
*333 23 ss id: 002 aaa bbb ccc
*22 233333333 34432 233 44
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Here's the output:

#Comment
*333 23 ss id: 002 aaa bbb ccc
*ss id addr id: 003 aaa bbb ccc
#Comment 2
*ss id addr id: 099 bbb ccc aaa
*22 233333333 34432 233 44
[download]