See my reply here Re^2: Hashes not working as expected

Try this demo

#!perl
use Data::Dumper;
my %hash = ( a=>{} );
if (  !exists $hash{'a'}{'b'}{'c'} ){};
print Dumper \%hash;
[download]

The problem is with exists creating intermediate levels

 foreach my $signalNm (keys %{$lastKnownSigValHRef->{$vcdFile}->{$signalId}}) {
    ### here
    if(!exists $inTimeRangeSignalsH{$vcdFile}{$signalNm}{$signalId}) {
     $sigsNotInTimeRangeH{$vcdFile}{$signalNm}{$signalId} = $lastKnownSigValHRef->{$vcdFile}->{$signalId}->{$signalNm}->{$hierScope}->[0];
    }
  }

I think you can fix it like this

foreach my $signalNm (keys %{$lastKnownSigValHRef->{$vcdFile}->{$signalId}}) {

  if (exists $inTimeRangeSignalsH{$vcdFile}{$signalNm}) {
    if (exists $inTimeRangeSignalsH{$vcdFile}{$signalNm}{$signalId}) {
      next;
    }
  }
  $sigsNotInTimeRangeH{$vcdFile}{$signalNm}{$signalId} 
  = $lastKnownSigValHRef->{$vcdFile}{$signalId}{$signalNm}{$hierScope}[0];

}

Update : Rather than returning variables from your methods you can encapsulate them into the object. For example, replacing the return statement from parseData with

#return(\%lastKnownSigValH, \%scopesHierH, \%scopesH, \%timeRangeH, 
 #       \%timeIntervalBasedActivityH, $vcdFile, $timeUnits);
 
  $self->{lastKnownSigValH} = \%lastKnownSigValH;
  $self->{scopesHierH} = \%scopesHierH; 
  $self->{scopesH}     = \%scopesH;
  $self->{timeRangeH}  = \%timeRangeH;
  $self->{timeIntervalBasedActivityH} = \%timeIntervalBasedActivityH; 
  $self->{vcdFile}   = $vcdFile; 
  $self->{timeUnits} = $timeUnits;
[download]

would allow you to write more readable code like this

#!/usr/bin/perl
use strict;
use warnings;
use diagnostics -verbose;

my $vcdFile = $ARGV[0];

my $datObj = Datafile->new();
$datObj->collectSignals($vcdFile);

package Datafile;
sub new {
  my $class = shift;
  my $self = {
    inTimeRangeSignalsH => {},
    sigsNotInTimeRangeH => {},
    timeRng   => {}, 
    hierScope => {},
  };
  return bless $self, $class;
}

sub collectSignals {
  my $self = shift;
  my $vcdFileOrig = shift; 
  
  $self->parseData($vcdFileOrig);
 
  if (exists $self->{timeRangeH}{$vcdFile}) {
    my $timeRng = $self->{timeRangeH}{$vcdFile}{'TIMERANGES'}[-1];
    $self->{timeRng}  = $timeRng; 

    if (exists $self->{timeIntervalBasedActivityH}{$vcdFile}) {
      my $hr1 = $self->{timeIntervalBasedActivityH}{$vcdFile};
      if (exists $hr1->{$timeRng}) {
        my $hr2 = $hr1->{$timeRng};
        for my $sigId (keys %$hr2) {
          for my $sigName (keys %{$hr2->{$sigId}}) {
            for my $scopeNm (keys %{$hr2->{$sigId}{$sigName}}) {
              if ( ($scopeNm =~ /_TB/) 
                && (exists $hr2->{$sigId}{$sigName}{$scopeNm}{'EXPANDE
+DVAL'}) ) {
                $self->{hierScope} = $scopeNm;
                my $sigValue =  $hr2->{$sigId}{$sigName}{$scopeNm}{'EX
+PANDEDVAL'}[-1];
                $self->{inTimeRangeSignalsH}{$vcdFile}{$sigName}{$sigI
+d}{$timeRng}{$scopeNm} = $sigValue;
              }
            }
          }
        }
      }
      foreach my $signal (keys %{$self->{inTimeRangeSignalsH}{$vcdFile
+}}) {
        print "Line 51 ::Dbg:: $signal $vcdFile\n";
      }
    }
  }
  
  if (exists $self->{lastKnownSigValH}{$vcdFile}) {
    my $hr1 = $self->{lastKnownSigValH}{$vcdFile};
    foreach my $signalId (keys %$hr1) {
      foreach my $signalNm (keys %{$hr1->{$signalId}}) {
        if (exists $self->{inTimeRangeSignalsH}{$vcdFile}{$signalNm}){
          if (exists $self->{inTimeRangeSignalsH}{$vcdFile}{$signalNm}
+{$signalId}){
            next;
          }
        }
        #if(!exists $self->{inTimeRangeSignalsH}{$vcdFile}{$signalNm}{
+$signalId}) {
        $self->{sigsNotInTimeRangeH}{$vcdFile}{$signalNm}{$signalId} 
             = $hr1->{$signalId}{$signalNm}{$self->{hierScope}}[0];
        #}
      }
    }
  }
 
  my $hr = $self->{inTimeRangeSignalsH};
  for my $vcdFile (keys %$hr) {
    for my $sig (keys %{$hr->{$vcdFile}}) {
      print "Line 75 ::Dbg:: $sig $vcdFile\n";
    }
  }
 
}
[download]

For debugging, it also allows you to dump all the data easily with

use Data::Dump 'pp';
pp $datObj;

poj

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