#!/usr/bin/perl

use warnings;
use strict;

my $del_qual;
while (<DATA>){
  if (/^\S/){
    if (/^\w+clk\[\d+\]/){
      $del_qual = 0;
    }
    else{
      $del_qual = 1;
    }
  }
  next if $del_qual and /\s+QUALIFIED/;
  print qq{$_};
}

__DATA__
qclk[6] INPUT (
     ! "asdk fd  sasd"
     VALID ( 
       late_lead 3 ar qclk slope 20
       late_lead 3 af qclk slope 04
       early_dn 8 ar qclk slope 6
       early_up 6 af qclk slope 6
     )
     cext %0.00394757
     cmax %0.005504
     QUALIFIED
)
clkout_qclk_61[3] OUTPUT (
)
clkout_qclk_61[2] OUTPUT (
     REQUIRED ( 
       earlyp  0.5 br qclk clm(2)
       latel_up  5 bf qclk clk(2)
     )
     REQUIRED ( 
       early_lead_dn  0.004 bf qclk clkdom(2)
       late_trail_dn  0.005 br qclk clkdom(2)
     )
     cext %0.0647336
     max_ceff_up %0.187
     QUALIFIED
)
[download]

qclk[6] INPUT (
     ! "asdk fd  sasd"
     VALID ( 
       late_lead 3 ar qclk slope 20
       late_lead 3 af qclk slope 04
       early_dn 8 ar qclk slope 6
       early_up 6 af qclk slope 6
     )
     cext %0.00394757
     cmax %0.005504
     QUALIFIED
)
clkout_qclk_61[3] OUTPUT (
)
clkout_qclk_61[2] OUTPUT (
     REQUIRED ( 
       earlyp  0.5 br qclk clm(2)
       latel_up  5 bf qclk clk(2)
     )
     REQUIRED ( 
       early_lead_dn  0.004 bf qclk clkdom(2)
       late_trail_dn  0.005 br qclk clkdom(2)
     )
     cext %0.0647336
     max_ceff_up %0.187
)
[download]

I personally believe that since the text you're operating on seems highly structured, and more precisely a proper language, then a fully reliable solution would comprise to write a parser. Perhaps one exists already. However, if you're fairly sure that the your data is regular enough then you may want to slurp it all at once and process it with somewhat naive regexen. The following program follows such an approach does work as expected on your sample, but be warned that it may fail on the full data.

use warnings;
use strict;

local $/ = "\n)\n";

while (<DATA>)
{
    my $got_end = chomp;
    s/\s*QUALIFIED$// unless m/^.*?clk\[\d+\]/;
    print;
    print $/ if $got_end; 
}
[download]

What is the simulation language you are working with? If it is widely used and the sort of editing you want to do is common it may be that there is already public domain code available.