Sorry, my last message was wrong, I put that thinking about the checkbox 
situation.
I think the following may be an answer:

sub set_multiselect_option {
         my ($form, $option_name, $non_null_value, $select) = @_;

# $form is the HTML::Form object
# $optin_name is the name of the options of the select input
# $non_null_value is the value that caracterizes the option
# $select: positive value to select, 0 or undef to uncheck the option

         my $target_input;

         foreach my $input ($form->inputs) {
                 my @possible_values = $input->possible_values;

                 if ($input->name eq $option_name and "@possible_values" =~ 
$non_null_value) {
                         $target_input = $input;
                         last;
                         }
                 }
         return unless $target_input;

         if ($select)    { $target_input->value($non_null_value); }
         else            { $target_input->value(undef); }
         }

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