my %ignore;

# First pass
while (<FH>) {
   $ignore{$1} = 1 if some_condition($_);
}

# Second pass
# reset the file to the beginning
seek FH, 0, 0;
while (<FH>) {
   if (m/matches interesting string with (capture)/) {
       if (exists($ignore{$1}) {
           next; # don't print this line
   print;
}

##</code><code>##

my $in_paragraph;
my $bar;
my %ignore;
while (<FH>) {
   if (m/start of paragraph/) {
       $in_paragraph = 1;
       $bar = 0
       next;
   }
   if (m/end of paragraph/) {
       $in_paragraph = 0;
       next;
   }
   if (m/line with bar/) {
       $bar = 1;
       next;
   }
   if (m/line with ref (\d+)/) {
       if ($begin and $bar and not $end) {
           $ignore{$1} = 1;
       }
       next;
   }
}