As soon as you get into nesting, you really need a parser. Fortunately, some properties of your data language allow us to construct one rather easily.

use strict;
use warnings;

sub process_para {
   my ($para) = @_;
   if (my ($id) = $para =~ /^(\w+)/) {
      if ($id ne 'blabla5') {
         $para =~ s/^TEXT TO BE REMOVED\n//mg;
      }
   }
   print($para);
}

{
   my ($depth, $buf);
   while (<DATA>) { 
      $buf .= $_;
      ++$depth if /\(\s*$/;
      --$depth if /^\s*\)\s*$/;
      #printf("[%d] %s", $depth, $_);
      if (!$depth) {
         process_para($buf);
         $buf = '';
      }
   }

   die("Bad nesting\n") if $depth;
}

__DATA__
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blabla_data[28] OUTPUT (
REQUIRED (
lead_up 0.193118 br fclk clkdom(3)
early_lea clkdom(3)
late_trail_dn -0.084738 br fclk clkdom(3)
late_tra
)
cext %0.00151055
min_ceff_up %0.034
TEXT TO BE REMOVED
)
blabla5 [145] OUTPUT (
REQUIRED (
early qclk clkdom(6)
early_l qclk clkdom(7)
late_trail_dn -0.125163 bf qclk clkdom(7)
late_t(7)
TEXT TO BE REMOVED
)
)
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Update: With the new data format, you'll need

sub process_para {
   my ($para) = @_;
   if (my ($id) = $para =~ /^ [ ]* (\S+)/x) {
      if ($id !~ /^.*clk\[\d\]\z/) {
         $para =~ s/^ [ ]* QUALIFIED [ ]* \n//xmg;
      }
   }
   print($para);
}
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