#!/usr/bin/perl

use strict;
use Data::Dumper;

my %hashOfArrays=( a=>[1,2,3], b=>[4,5,6], c=>[7,8,9] );
my %toDelete=( a=>2, b=>6, c=>8 );
for my $array (keys %hashOfArrays) { 
   if ($toDelete{$array}) {   
      $hashOfArrays{$array}=[ 
        grep { $_ != $toDelete{$array} }   
           @{$hashOfArrays{$array}} 
      ];
   }
}
print Dumper(\%hashOfArrays);  
# prints $VAR1 = {
#          'c' => [
#                   7,
#                   9
#                 ],
#          'a' => [
#                   1,
#                   3
#                 ],
#          'b' => [
#                   4,
#                   5
#                 ]
#        };
exit;