for ( my $indx = 0; $indx <=2; $indx++){
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That is usually written as:

    for my $indx ( 0 .. 2 ) {
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        # Make a reference to the hash reference 
         my $work_package = \%{$work_request};
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You have a hash reference in $work_request which you then dereference as %{$work_request} and then get a reference to the original hash with \%{$work_request}.   You can accomplish the same thing more simply with:

         my $work_package = $work_request;
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            my @list = @{$work_package->{$key}};
            for (my $a_id=0; $a_id <= $#list; $a_id++) {
                $list[$a_id]=$indx;
                print " $list[$a_id]\t";
            }
            print "\n";
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You are copying the contents of @{$work_package->{$key}} to @list so any changes to the contents of @list will disapear when the loop ends.   The for loop is usually written as:

            for my $a_id ( 0 .. $#list ) {
                $list[$a_id]=$indx;
                print " $list[$a_id]\t";
            }
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