This is indeed a problem.. I've encountered it myself after creating half a zillion checkboxes and then wanting to perform delete operations on the unchecked fields.

There may be better solutions, but one way I might approach this is to create (for every checkbox) a hidden field with a similar name to the name assigned for the checkbox. If my checkbox name was name="checkbox_284" then I'd name my hidden field name="hidden_checkbox_284".

In my CGI form I'd have a loop that goes something like:

  foreach my $param ( $cgi->param ) {
      next if ( $param !~ m/^hidden_(.+)$/ );
      my $checkboxname=$1;

      if ( ! $cgi->param( $checkboxname ) ) {
          # delete this item
      } else {
          # add this item
      }
  }
[download]

update: So that, even if the browser doesn't send the checkbox parameters for the unchecked fields, at least the browser sends all the hidden fields and I can then use them to check for the existance of the checkbox field.